16-89613079-T-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613079
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613079
    reference: chr 16
allele count: 2
allele frequency: 1.650628063978344e-5
allele num: 121166
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.189T>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1463T>G
  hgvsp: ENSP00000268704.2:p.Ile488Ser
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.61T>G
  hgvsp: ENSP00000457298.1:p.Ile21Ser
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*136T>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.8T>G
  hgvsp: ENSP00000457387.1:p.Ile3Ser
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: VQSRTrancheSNP99.95to100.00
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2533
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1580
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 101
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1732
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3326
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1562
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4367
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1719
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5603
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6532
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9332
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1854
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6862
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1754
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8034
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2043
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1671
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2955
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2154
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7339
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 52
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4091
  bin: 6.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1846
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 67
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 42
  bin: 3.75e1
  variant carriers: 0
hgvs: p.Ile488Ser
num of homozygotes: 0
population: East Asian
population: European (Finnish)
population: Other
population: Latino
population: African
population: South Asian
population: European (Non-Finnish)
reference allele: T
site quality: FS
site quality: DP
site quality: BaseQRankSum
site quality: MQRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: QD
site quality: InbreedingCoeff
site quality: ClippingRankSum

16-89613084-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613084
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613084
    reference: chr 16
allele count: 1
allele frequency: 8.331250520703158e-6
allele num: 120030
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.13G>A
  hgvsp: ENSP00000457387.1:p.Glu5Lys
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.66G>A
  hgvsp: ENSP00000457298.1:p.Glu23Lys
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.194G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1468G>A
  hgvsp: ENSP00000268704.2:p.Glu490Lys
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*141G>A
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: VQSRTrancheSNP99.90to99.95
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1853
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3331
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9342
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4365
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1690
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1577
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6856
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5598
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8019
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2021
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1719
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6537
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2516
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 89
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1590
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1758
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1745
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 57
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 42
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34566
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 594
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4070
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2125
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 82
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 48
  bin: 5.75e1
  variant carriers: 0
hgvs: p.Glu490Lys
num of homozygotes: 0
population: South Asian
population: Latino
population: Other
population: African
population: East Asian
population: European (Finnish)
population: European (Non-Finnish)
reference allele: G
site quality: FS
site quality: ReadPosRankSum
site quality: QD
site quality: MQRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: MQ
site quality: InbreedingCoeff
site quality: DP
site quality: BaseQRankSum

16-89613084-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613084
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613084
    reference: chr 16
allele count: 7
allele frequency: 5.83187536449221e-5
allele num: 120030
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: stop_gained
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1468G>T
  hgvsp: ENSP00000268704.2:p.Glu490Ter
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*141G>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: stop_gained
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.66G>T
  hgvsp: ENSP00000457298.1:p.Glu23Ter
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.194G>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: stop_gained
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.13G>T
  hgvsp: ENSP00000457387.1:p.Glu5Ter
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: stop gained
filter: VQSRTrancheSNP99.90to99.95
genotype depth: GenotypeDepth
  all individuals: 8019
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 89
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1690
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 6537
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4365
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 5598
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3331
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1719
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2021
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1745
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6856
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1590
  bin: 8.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1758
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9342
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1577
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2516
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1853
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4070
  bin: 6.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 7326
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34566
  bin: 9.75e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 2.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 52
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 4.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 48
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3327
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 42
  bin: 5.25e1
  variant carriers: 0
hgvs: p.Glu490Ter
num of homozygotes: 0
population: African
population: Latino
population: Other
population: European (Finnish)
population: European (Non-Finnish)
population: East Asian
population: South Asian
reference allele: G
site quality: VQSLOD
site quality: FS
site quality: ClippingRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: DP
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: MQRankSum
site quality: QD

16-89613100-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613100
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613100
    reference: chr 16
allele count: 2
allele frequency: 1.648233917357551e-5
allele num: 121342
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.82G>C
  hgvsp: ENSP00000457298.1:p.Ser28Thr
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.210G>C
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.29G>C
  hgvsp: ENSP00000457387.1:p.Ser10Thr
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1484G>C
  hgvsp: ENSP00000268704.2:p.Ser495Thr
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*157G>C
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1533
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9188
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 3322
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1668
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1839
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6757
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4383
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1540
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1796
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1687
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5651
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6941
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1980
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2487
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1621
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8186
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2964
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 54
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3581
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2180
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4178
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34820
  bin: 9.75e1
  variant carriers: 2
hgvs: p.Ser495Thr
num of homozygotes: 0
population: Other
population: Latino
population: African
population: European (Finnish)
population: East Asian
population: European (Non-Finnish)
population: South Asian
reference allele: G
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: DP
site quality: MQRankSum
site quality: QD
site quality: ClippingRankSum
site quality: MQ

16-89613101-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613101
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613101
    reference: chr 16
allele count: 1
allele frequency: 8.241169586787756e-6
allele num: 121342
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.30C>T
  hgvsp: ENST00000561911.1:c.30C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*158C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.83C>T
  hgvsp: ENST00000566221.1:c.83C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.211C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1485C>T
  hgvsp: ENST00000268704.2:c.1485C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3323
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6938
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1686
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1980
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1797
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1540
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6762
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4382
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1622
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2486
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 42
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1668
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9188
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1533
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8187
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1837
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5652
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7594
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2180
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3582
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34819
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Ser495Ser
num of homozygotes: 0
population: African
population: South Asian
population: Other
population: European (Finnish)
population: European (Non-Finnish)
population: East Asian
population: Latino
reference allele: C
site quality: QD
site quality: FS
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: BaseQRankSum
site quality: VQSLOD
site quality: MQ

16-89613102-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613102
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613102
    reference: chr 16
allele count: 1
allele frequency: 8.241305422778968e-6
allele num: 121340
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.212C>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*159C>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.84C>G
  hgvsp: ENSP00000457298.1:p.Leu29Val
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1486C>G
  hgvsp: ENSP00000268704.2:p.Leu496Val
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.31C>G
  hgvsp: ENSP00000457387.1:p.Leu11Val
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3323
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1841
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1533
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6936
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6768
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4381
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8187
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1540
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1686
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1797
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2486
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5651
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1621
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9188
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1668
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1981
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2964
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7601
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34819
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3585
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1862
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 50
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Leu496Val
num of homozygotes: 0
population: African
population: South Asian
population: European (Non-Finnish)
population: East Asian
population: Latino
population: European (Finnish)
population: Other
reference allele: C
site quality: MQ
site quality: BaseQRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: QD
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: FS
site quality: DP

16-89613113-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613113
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613113
    reference: chr 16
allele count: 1
allele frequency: 8.240354664864776e-6
allele num: 121354
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.223C>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1497C>G
  hgvsp: ENST00000268704.2:c.1497C>G(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.42C>G
  hgvsp: ENST00000561911.1:c.42C>G(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.95C>G
  hgvsp: ENST00000566221.1:c.95C>G(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*170C>G
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1797
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6768
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3323
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1979
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1533
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8192
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1845
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6939
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 9187
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1621
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2487
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1668
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4382
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1686
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5650
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1540
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2966
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3586
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2182
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7602
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34819
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4186
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 44
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Thr499Thr
num of homozygotes: 0
population: East Asian
population: African
population: European (Non-Finnish)
population: Latino
population: European (Finnish)
population: Other
population: South Asian
reference allele: C
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: MQ
site quality: FS
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: DP
site quality: ClippingRankSum
site quality: QD

16-89613116-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613116
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613116
    reference: chr 16
allele count: 1
allele frequency: 8.240354664864776e-6
allele num: 121354
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.98G>A
  hgvsp: ENST00000566221.1:c.98G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1500G>A
  hgvsp: ENST00000268704.2:c.1500G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.226G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*173G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.45G>A
  hgvsp: ENST00000561911.1:c.45G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6940
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2487
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1979
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4381
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5651
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1686
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1668
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1540
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8192
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6772
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1845
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1796
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3322
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9188
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1621
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1533
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3585
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7604
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34820
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3376
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1861
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Gln500Gln
num of homozygotes: 0
population: Latino
population: African
population: European (Non-Finnish)
population: South Asian
population: East Asian
population: Other
population: European (Finnish)
reference allele: G
site quality: QD
site quality: MQRankSum
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: DP
site quality: VQSLOD
site quality: FS
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: MQ

16-89613123-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613123
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613123
    reference: chr 16
allele count: 18290
allele frequency: 1.507136029532944e-1
allele num: 121356
alternate allele: G
annotation: Annotation
  canonical: false
  clinical significance: likely_benign
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.233A>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  clinical significance: likely_benign
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1507A>G
  hgvsp: ENSP00000268704.2:p.Thr503Ala
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  clinical significance: likely_benign
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.52A>G
  hgvsp: ENSP00000457387.1:p.Thr18Ala
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  clinical significance: likely_benign
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.105A>G
  hgvsp: ENSP00000457298.1:p.Thr36Ala
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  clinical significance: likely_benign
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*180A>G
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 6688
  bin: 2.75e1
  variant carriers: 54
genotype depth: GenotypeDepth
  all individuals: 1051
  bin: 7.25e1
  variant carriers: 267
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2112
  bin: 5.75e1
  variant carriers: 122
genotype depth: GenotypeDepth
  all individuals: 1575
  bin: 6.25e1
  variant carriers: 159
genotype depth: GenotypeDepth
  all individuals: 8105
  bin: 3.25e1
  variant carriers: 72
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 7.5e0
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 55
  bin: 1.75e1
  variant carriers: 30
genotype depth: GenotypeDepth
  all individuals: 931
  bin: 8.75e1
  variant carriers: 514
genotype depth: GenotypeDepth
  all individuals: 1233
  bin: 6.75e1
  variant carriers: 205
genotype depth: GenotypeDepth
  all individuals: 4181
  bin: 4.75e1
  variant carriers: 86
genotype depth: GenotypeDepth
  all individuals: 5552
  bin: 4.25e1
  variant carriers: 93
genotype depth: GenotypeDepth
  all individuals: 1742
  bin: 2.25e1
  variant carriers: 31
genotype depth: GenotypeDepth
  all individuals: 36
  bin: 1.25e1
  variant carriers: 8
genotype depth: GenotypeDepth
  all individuals: 969
  bin: 8.25e1
  variant carriers: 431
genotype depth: GenotypeDepth
  all individuals: 3067
  bin: 5.25e1
  variant carriers: 94
genotype depth: GenotypeDepth
  all individuals: 14677
  bin: 9.75e1
  variant carriers: 13576
genotype depth: GenotypeDepth
  all individuals: 945
  bin: 7.75e1
  variant carriers: 338
genotype depth: GenotypeDepth
  all individuals: 6862
  bin: 3.75e1
  variant carriers: 74
genotype depth: GenotypeDepth
  all individuals: 903
  bin: 9.25e1
  variant carriers: 566
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 3.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 3.25e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 5.75e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 1717
  bin: 8.75e1
  variant carriers: 4
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 4.75e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 4.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 2.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 7317
  bin: 6.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 2795
  bin: 9.25e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Thr503Ala
num of homozygotes: 1571
population: European (Non-Finnish)
population: Other
population: South Asian
population: East Asian
population: African
population: European (Finnish)
population: Latino
reference allele: A
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: DP
site quality: QD
site quality: MQRankSum
site quality: VQSLOD
site quality: FS

16-89613128-T-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613128
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613128
    reference: chr 16
allele count: 1
allele frequency: 8.240083060037246e-6
allele num: 121358
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*185T>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.238T>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.110T>G
  hgvsp: ENSP00000457298.1:p.Phe37Leu
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1512T>G
  hgvsp: ENSP00000268704.2:p.Phe504Leu
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.57T>G
  hgvsp: ENSP00000457387.1:p.Phe19Leu
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 9179
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 979
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 559
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 56
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2454
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11723
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5257
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7280
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3763
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1264
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 709
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 762
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10273
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2462
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1694
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1743
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 475
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5872
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25357
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2306
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2878
  bin: 7.25e1
  variant carriers: 0
hgvs: p.Phe504Leu
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: East Asian
population: African
population: South Asian
population: Other
population: European (Non-Finnish)
reference allele: T
site quality: DP
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: FS
site quality: MQRankSum
site quality: MQ
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: QD

16-89613132-T-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613132
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613132
    reference: chr 16
allele count: 1
allele frequency: 8.240218860212928e-6
allele num: 121356
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1516T>A
  hgvsp: ENSP00000268704.2:p.Ser506Thr
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.61T>A
  hgvsp: ENSP00000457387.1:p.Ser21Thr
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*189T>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.242T>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.114T>A
  hgvsp: ENSP00000457298.1:p.Ser39Thr
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2462
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 762
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3763
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1264
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 979
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7280
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 475
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10274
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11716
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5257
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 55
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 559
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1743
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 709
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2462
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9180
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1693
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4413
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2305
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4742
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25356
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5872
  bin: 6.75e1
  variant carriers: 0
hgvs: p.Ser506Thr
num of homozygotes: 0
population: East Asian
population: European (Non-Finnish)
population: Latino
population: European (Finnish)
population: Other
population: African
population: South Asian
reference allele: T
site quality: FS
site quality: MQ
site quality: MQRankSum
site quality: BaseQRankSum
site quality: QD
site quality: DP
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: VQSLOD

16-89613134-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613134
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613134
    reference: chr 16
allele count: 6
allele frequency: 4.944212798918866e-5
allele num: 121354
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.244C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1518C>T
  hgvsp: ENST00000268704.2:c.1518C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*191C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.116C>T
  hgvsp: ENST00000566221.1:c.116C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.63C>T
  hgvsp: ENST00000561911.1:c.63C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 558
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1743
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9181
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7278
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 762
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 56
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1264
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2462
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3763
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2462
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1694
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 710
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 477
  bin: 9.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 10279
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 979
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11713
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5256
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 52
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2305
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2875
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4741
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5869
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Ser506Ser
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: South Asian
population: European (Non-Finnish)
population: Other
population: East Asian
population: African
reference allele: C
site quality: BaseQRankSum
site quality: FS
site quality: ClippingRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: DP
site quality: QD
site quality: MQ

16-89613139-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613139
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613139
    reference: chr 16
allele count: 7
allele frequency: 5.768533473975673e-5
allele num: 121348
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*196G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.121G>A
  hgvsp: ENSP00000457298.1:p.Arg41His
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.249G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1523G>A
  hgvsp: ENSP00000268704.2:p.Arg508His
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.68G>A
  hgvsp: ENSP00000457387.1:p.Arg23His
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 709
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2461
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 64
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10280
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5256
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2458
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3762
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 475
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 978
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 762
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1694
  bin: 9.75e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 9180
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11720
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7277
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1263
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1742
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 557
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3794
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5869
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25346
  bin: 9.75e1
  variant carriers: 7
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11187
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2307
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 55
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 4.75e1
  variant carriers: 0
hgvs: p.Arg508His
num of homozygotes: 0
population: European (Non-Finnish)
population: Other
population: European (Finnish)
population: South Asian
population: East Asian
population: Latino
population: African
reference allele: G
site quality: ClippingRankSum
site quality: FS
site quality: VQSLOD
site quality: DP
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: QD
site quality: BaseQRankSum

16-89613145-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613145
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613145
    reference: chr 16
allele count: 306
allele frequency: 2.521673204337937e-3
allele num: 121348
alternate allele: T
annotation: Annotation
  canonical: false
  clinical significance: pathogenic
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.74C>T
  hgvsp: ENSP00000457387.1:p.Ala25Val
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  clinical significance: pathogenic
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1529C>T
  hgvsp: ENSP00000268704.2:p.Ala510Val
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  clinical significance: pathogenic
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.127C>T
  hgvsp: ENSP00000457298.1:p.Ala43Val
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  clinical significance: pathogenic
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.255C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  clinical significance: pathogenic
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*202C>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 9170
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1721
  bin: 6.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 476
  bin: 9.25e1
  variant carriers: 15
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11706
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1839
  bin: 9.75e1
  variant carriers: 225
genotype depth: GenotypeDepth
  all individuals: 10272
  bin: 2.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 71
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3749
  bin: 5.25e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 1252
  bin: 6.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 5240
  bin: 4.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 2462
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 964
  bin: 7.25e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 705
  bin: 8.25e1
  variant carriers: 11
genotype depth: GenotypeDepth
  all individuals: 758
  bin: 7.75e1
  variant carriers: 13
genotype depth: GenotypeDepth
  all individuals: 7260
  bin: 4.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 556
  bin: 8.75e1
  variant carriers: 12
genotype depth: GenotypeDepth
  all individuals: 2444
  bin: 5.75e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 4407
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3790
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11191
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4737
  bin: 7.75e1
  variant carriers: 0
hgvs: p.Ala510Val
num of homozygotes: 2
population: East Asian
population: European (Finnish)
population: South Asian
population: European (Non-Finnish)
population: Other
population: African
population: Latino
reference allele: C
site quality: MQ
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: DP
site quality: QD
site quality: ClippingRankSum
site quality: BaseQRankSum

16-89613160-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613160
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613160
    reference: chr 16
allele count: 2
allele frequency: 1.648587160803192e-5
allele num: 121316
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.142G>A
  hgvsp: ENSP00000457298.1:p.Gly48Glu
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.89G>A
  hgvsp: ENSP00000457387.1:p.Gly30Glu
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*217G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1544G>A
  hgvsp: ENSP00000268704.2:p.Gly515Glu
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.270G>A
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 960
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10308
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2452
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11758
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1724
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 464
  bin: 9.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 3767
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2450
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 97
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7308
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1255
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9216
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5262
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 697
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1619
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 745
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11229
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2312
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3808
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2884
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 82
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 37
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5871
  bin: 6.75e1
  variant carriers: 0
hgvs: p.Gly515Glu
num of homozygotes: 0
population: South Asian
population: Latino
population: East Asian
population: European (Non-Finnish)
population: Other
population: European (Finnish)
population: African
reference allele: G
site quality: MQ
site quality: QD
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: DP

16-89613161-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613161
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613161
    reference: chr 16
allele count: 1
allele frequency: 8.243207596940122e-6
allele num: 121312
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.143A>G
  hgvsp: ENST00000566221.1:c.143A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*218A>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.271A>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1545A>G
  hgvsp: ENST00000268704.2:c.1545A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.90A>G
  hgvsp: ENST00000561911.1:c.90A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 10303
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 745
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2452
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11759
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2441
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1724
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1254
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7308
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1620
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5262
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9216
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 462
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3767
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 960
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 697
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 39
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4433
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2313
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 91
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5871
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2883
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11207
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4760
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Gly515Gly
num of homozygotes: 0
population: Latino
population: South Asian
population: Other
population: European (Non-Finnish)
population: European (Finnish)
population: African
population: East Asian
reference allele: A
site quality: FS
site quality: VQSLOD
site quality: ClippingRankSum
site quality: DP
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: MQRankSum
site quality: QD
site quality: InbreedingCoeff
site quality: MQ

16-89613169-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613169
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613169
    reference: chr 16
allele count: 4
allele frequency: 3.298098646130506e-5
allele num: 121282
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: splice_donor_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.150+1G>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_donor_variant
  consequence: non_coding_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.278+1G>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_donor_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*225+1G>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: splice_donor_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1552+1G>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_donor_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.97+1G>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: splice donor
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 136
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3766
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11759
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 959
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9213
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 745
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2451
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1621
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 2400
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5261
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10274
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 68
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1254
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 699
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 463
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1723
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7309
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5859
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3810
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11168
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 56
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4429
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 5.25e1
  variant carriers: 0
hgvs: c.1552+1G>T
num of homozygotes: 0
population: Latino
population: European (Non-Finnish)
population: South Asian
population: European (Finnish)
population: East Asian
population: Other
population: African
reference allele: G
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: FS
site quality: MQ
site quality: DP
site quality: QD

16-89613170-T-TACGTTCTC
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613170
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613178
    reference: chr 16
allele count: 1
allele frequency: 8.245382585751979e-6
allele num: 121280
alternate allele: TACGTTCTC
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2393
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2451
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 745
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11755
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1254
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5262
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 959
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7309
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10270
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3766
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1724
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1619
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 697
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9214
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 462
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4430
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 48
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2876
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 124
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11155
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2312
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25196
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 1.25e1
  variant carriers: 0
hgvs: c.1552+4_1552+11dupCGTTCTCA
num of homozygotes: 0
population: East Asian
population: African
population: Other
population: South Asian
population: European (Non-Finnish)
population: Latino
population: European (Finnish)
reference allele: T
site quality: QD
site quality: VQSLOD
site quality: BaseQRankSum
site quality: DP
site quality: MQRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: FS
site quality: ClippingRankSum

16-89613172-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613172
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613172
    reference: chr 16
allele count: 1
allele frequency: 8.245790523937529e-6
allele num: 121274
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.278+4C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.150+4C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1552+4C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*225+4C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.97+4C>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1723
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11743
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 697
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2386
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9212
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1254
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5261
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7309
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3766
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 165
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2451
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10260
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 959
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 462
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1619
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 745
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 85
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 65
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3811
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5862
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2873
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 136
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4752
  bin: 7.75e1
  variant carriers: 0
hgvs: c.1552+4C>T
num of homozygotes: 0
population: Latino
population: East Asian
population: European (Non-Finnish)
population: South Asian
population: European (Finnish)
population: African
population: Other
reference allele: C
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: QD
site quality: MQRankSum
site quality: FS
site quality: VQSLOD
site quality: DP
site quality: MQ
site quality: ReadPosRankSum

16-89613173-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613173
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613173
    reference: chr 16
allele count: 2
allele frequency: 1.649158104787506e-5
allele num: 121274
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.97+5G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1552+5G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.278+5G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*225+5G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.150+5G>A
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 85
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2389
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11738
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 697
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 463
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 9213
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10261
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3765
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2451
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 745
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7309
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 958
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5262
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1618
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1723
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1254
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 64
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25195
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4427
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3811
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4752
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5859
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 4.25e1
  variant carriers: 0
hgvs: c.1552+5G>A
num of homozygotes: 0
population: East Asian
population: Latino
population: Other
population: South Asian
population: African
population: European (Finnish)
population: European (Non-Finnish)
reference allele: G
site quality: MQRankSum
site quality: FS
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: DP
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: QD

16-89613177-T-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613177
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613177
    reference: chr 16
allele count: 4
allele frequency: 3.298860243785772e-5
allele num: 121254
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*225+9T>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.97+9T>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.150+9T>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1552+9T>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.278+9T>A
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 70
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2359
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7309
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9211
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 111
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10234
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 698
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 5261
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1723
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11735
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2449
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1618
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 745
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3767
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 958
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 462
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1254
  bin: 6.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2873
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 77
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 58
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 164
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4426
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5851
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
num of homozygotes: 0
population: European (Finnish)
population: African
population: Latino
population: South Asian
population: European (Non-Finnish)
population: Other
population: East Asian
reference allele: T
site quality: InbreedingCoeff
site quality: QD
site quality: MQRankSum
site quality: BaseQRankSum
site quality: MQ
site quality: ClippingRankSum
site quality: VQSLOD
site quality: FS
site quality: ReadPosRankSum
site quality: DP

16-89613179-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613179
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613179
    reference: chr 16
allele count: 1
allele frequency: 8.247966876165026e-6
allele num: 121242
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*225+11A>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.278+11A>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1552+11A>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.150+11A>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.97+11A>G
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 129
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5258
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1253
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 746
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 9211
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 217
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7306
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1723
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 957
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2354
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10220
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11716
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 697
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3766
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 462
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1618
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2450
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25189
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 2314
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 68
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2874
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4424
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3809
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 183
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 5.75e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: East Asian
population: European (Finnish)
population: South Asian
population: Latino
population: Other
reference allele: A
site quality: FS
site quality: ReadPosRankSum
site quality: MQ
site quality: VQSLOD
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: QD

http://identifiers.org/exac.variant/16-89613183-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613183
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613183
    reference: chr 16
allele count: 5
allele frequency: 4.125684863687372e-5
allele num: 121192
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.97+15C>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.278+15C>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*225+15C>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1552+15C>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.150+15C>A
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 89
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1253
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1722
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 697
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7304
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 11682
  bin: 3.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 2449
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 154
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9199
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 272
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 463
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 746
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1618
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2336
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10189
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 957
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5252
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3774
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 221
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 4.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 106
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 66
  bin: 3.75e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 92
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4419
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2865
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10934
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2309
  bin: 8.75e1
  variant carriers: 0
num of homozygotes: 0
population: Other
population: South Asian
population: European (Finnish)
population: Latino
population: European (Non-Finnish)
population: African
population: East Asian
reference allele: C
site quality: VQSLOD
site quality: MQRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: QD
site quality: ReadPosRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: DP

16-89613183-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613183
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613183
    reference: chr 16
allele count: 2
allele frequency: 1.650273945474949e-5
allele num: 121192
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*225+15C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.97+15C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.150+15C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.278+15C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1552+15C>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 697
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 272
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 89
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11682
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7304
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5252
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 957
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2449
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2336
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3774
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 154
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 746
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 463
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1618
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9199
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10189
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1722
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1253
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25169
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 2865
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 221
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5830
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10934
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 66
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 106
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4743
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 92
  bin: 2.75e1
  variant carriers: 0
num of homozygotes: 0
population: Latino
population: Other
population: European (Non-Finnish)
population: African
population: South Asian
population: European (Finnish)
population: East Asian
reference allele: C
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: FS
site quality: QD
site quality: VQSLOD
site quality: MQ
site quality: MQRankSum
site quality: DP

16-89613184-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613184
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613184
    reference: chr 16
allele count: 3
allele frequency: 2.476064707824365e-5
allele num: 121160
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*225+16G>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.150+16G>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1552+16G>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.278+16G>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.97+16G>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 197
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9167
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1252
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7285
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 365
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 745
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 5250
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10166
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 110
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2447
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 957
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3762
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2319
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 697
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1722
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1618
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11632
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 462
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5760
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 112
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 83
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3804
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 95
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 146
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10754
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 288
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4408
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2306
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 121
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 1.25e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: Latino
population: African
population: European (Non-Finnish)
population: European (Finnish)
population: Other
population: South Asian
reference allele: G
site quality: ClippingRankSum
site quality: MQ
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: FS
site quality: InbreedingCoeff
site quality: DP
site quality: QD
site quality: BaseQRankSum

16-89613194-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613194
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613194
    reference: chr 16
allele count: 4
allele frequency: 3.303491790822899e-5
allele num: 121084
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.278+26C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1552+26C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.150+26C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.97+26C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*225+26C>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 462
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11452
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5244
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 144
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3761
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 593
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 350
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9104
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2294
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7255
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10056
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 697
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 958
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2445
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1722
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 743
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1252
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1618
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 138
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10614
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4702
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25154
  bin: 9.75e1
  variant carriers: 4
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 48
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 242
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 172
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2815
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 56
  bin: 5.75e1
  variant carriers: 0
num of homozygotes: 0
population: European (Finnish)
population: Latino
population: Other
population: African
population: South Asian
population: East Asian
population: European (Non-Finnish)
reference allele: C
site quality: QD
site quality: BaseQRankSum
site quality: MQRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: DP
site quality: MQ
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: FS

16-89613195-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613195
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613195
    reference: chr 16
allele count: 1
allele frequency: 8.259275166011431e-6
allele num: 121076
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.150+27A>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*225+27A>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1552+27A>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.278+27A>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.97+27A>G
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 381
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 698
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2295
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11408
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7250
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 643
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10028
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9098
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1252
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3761
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1616
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2445
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1722
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 959
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 147
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 462
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5242
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 743
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3797
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 156
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 261
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5702
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 188
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 465
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2812
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 55
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10557
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 38
  bin: 5.25e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: East Asian
population: South Asian
population: European (Finnish)
population: European (Non-Finnish)
population: Latino
population: Other
reference allele: A
site quality: FS
site quality: VQSLOD
site quality: MQ
site quality: QD
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: DP
site quality: BaseQRankSum
site quality: MQRankSum
site quality: ReadPosRankSum

16-89613198-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613198
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613198
    reference: chr 16
allele count: 3
allele frequency: 2.478642364955302e-5
allele num: 121034
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.278+30G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.150+30G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.97+30G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*225+30G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1552+30G>A
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 11192
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3761
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1723
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 160
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 825
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2444
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 959
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1616
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1251
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9838
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2274
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 698
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 671
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5241
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 743
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 462
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7245
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9044
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 398
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 124
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 269
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 553
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5602
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10046
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 117
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25149
  bin: 9.75e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 112
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2783
  bin: 7.25e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: South Asian
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
population: East Asian
population: Other
reference allele: G
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: MQRankSum
site quality: DP
site quality: ReadPosRankSum
site quality: FS
site quality: BaseQRankSum
site quality: VQSLOD
site quality: QD

16-89613203-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613203
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613203
    reference: chr 16
allele count: 7
allele frequency: 5.785123966942149e-5
allele num: 121000
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.278+35G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.97+35G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1552+35G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.150+35G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*225+35G>A
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 743
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1183
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 959
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9515
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3762
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10889
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7227
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5229
  bin: 4.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 178
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1723
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2443
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2323
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8977
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 462
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1616
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 968
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1250
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 698
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25136
  bin: 9.75e1
  variant carriers: 7
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 112
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5539
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 560
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2289
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9519
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2758
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 438
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 195
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 345
  bin: 2.75e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: African
population: European (Finnish)
population: South Asian
population: Other
population: European (Non-Finnish)
population: Latino
reference allele: G
site quality: ReadPosRankSum
site quality: FS
site quality: VQSLOD
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: MQ
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: QD

16-89613212-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613212
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613212
    reference: chr 16
allele count: 1
allele frequency: 8.275131574592036e-6
allele num: 120844
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.97+44G>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.150+44G>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*225+44G>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1552+44G>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.278+44G>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2345
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 698
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1249
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8825
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1616
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 230
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3760
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8374
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2444
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5219
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3332
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 997
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7192
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1722
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 959
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 462
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 743
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9972
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7650
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 555
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 42
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 659
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 921
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 59
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5152
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 165
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 847
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 440
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2273
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 497
  bin: 5.25e1
  variant carriers: 0
num of homozygotes: 0
population: European (Non-Finnish)
population: European (Finnish)
population: South Asian
population: Latino
population: African
population: Other
population: East Asian
reference allele: G
site quality: VQSLOD
site quality: MQRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: FS
site quality: DP

16-89613218-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89613218
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89613218
    reference: chr 16
allele count: 398
allele frequency: 3.3003300330033e-3
allele num: 120594
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1552+50G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.150+50G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*225+50G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.97+50G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.278+50G>A
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1006
  bin: 1.25e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 8753
  bin: 3.75e1
  variant carriers: 53
genotype depth: GenotypeDepth
  all individuals: 697
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2447
  bin: 5.75e1
  variant carriers: 17
genotype depth: GenotypeDepth
  all individuals: 961
  bin: 7.25e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 5212
  bin: 4.75e1
  variant carriers: 39
genotype depth: GenotypeDepth
  all individuals: 9305
  bin: 3.25e1
  variant carriers: 71
genotype depth: GenotypeDepth
  all individuals: 2310
  bin: 1.75e1
  variant carriers: 13
genotype depth: GenotypeDepth
  all individuals: 460
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1723
  bin: 6.25e1
  variant carriers: 11
genotype depth: GenotypeDepth
  all individuals: 7158
  bin: 4.25e1
  variant carriers: 58
genotype depth: GenotypeDepth
  all individuals: 1621
  bin: 9.75e1
  variant carriers: 9
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 271
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3760
  bin: 5.25e1
  variant carriers: 26
genotype depth: GenotypeDepth
  all individuals: 4858
  bin: 2.25e1
  variant carriers: 29
genotype depth: GenotypeDepth
  all individuals: 742
  bin: 7.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 7603
  bin: 2.75e1
  variant carriers: 43
genotype depth: GenotypeDepth
  all individuals: 1251
  bin: 6.75e1
  variant carriers: 6
genotype quality: GenotypeQuality
  all individuals: 4420
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 154
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 570
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 47
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 894
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 445
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 665
  bin: 5.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1919
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 68
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 737
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4471
  bin: 6.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 5336
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2559
  bin: 7.25e1
  variant carriers: 1
num of homozygotes: 6
population: European (Finnish)
population: European (Non-Finnish)
population: African
population: East Asian
population: Other
population: Latino
population: South Asian
reference allele: G
site quality: FS
site quality: DP
site quality: QD
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: VQSLOD

16-89614370-A-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614370
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614370
    reference: chr 16
allele count: 1
allele frequency: 8.315870006320061e-6
allele num: 120252
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.279-41A>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.98-41A>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*226-41A>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.151-41A>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1553-41A>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 84
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3396
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 484
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7851
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 836
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 266
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 807
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14784
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 557
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 581
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1315
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1702
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3658
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2384
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 492
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 350
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14361
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1057
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4969
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 768
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 37
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3289
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 296
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 141
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 335
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 207
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 71
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8844
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1532
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3409
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20718
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 40
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.5e0
  variant carriers: 0
num of homozygotes: 0
population: Latino
population: South Asian
population: European (Non-Finnish)
population: African
population: European (Finnish)
population: Other
population: East Asian
reference allele: A
site quality: QD
site quality: MQ
site quality: BaseQRankSum
site quality: FS
site quality: ReadPosRankSum
site quality: DP
site quality: MQRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: InbreedingCoeff

16-89614379-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614379
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614379
    reference: chr 16
allele count: 1
allele frequency: 8.315455104857889e-6
allele num: 120258
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.279-32C>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.151-32C>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1553-32C>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*226-32C>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.98-32C>G
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 14365
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 430
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 492
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4969
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 477
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3787
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1702
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1057
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2383
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 807
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 80
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 747
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3396
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14881
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1314
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7851
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 767
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 581
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 351
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 266
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1533
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 273
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20867
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13958
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 118
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 96
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3404
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 70
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 151
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 210
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 279
  bin: 3.75e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: South Asian
population: East Asian
population: European (Non-Finnish)
population: Latino
population: European (Finnish)
population: Other
reference allele: C
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: FS
site quality: VQSLOD
site quality: BaseQRankSum
site quality: DP
site quality: MQ
site quality: MQRankSum
site quality: QD

16-89614381-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614381
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614381
    reference: chr 16
allele count: 1
allele frequency: 8.314348903337379e-6
allele num: 120274
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1553-30C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.151-30C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.98-30C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.279-30C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*226-30C>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 7847
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4969
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 266
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1702
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 471
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 720
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3830
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14368
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 581
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3395
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2384
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 79
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1057
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 807
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 492
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1314
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 401
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14902
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 351
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 767
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 68
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 69
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 640
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 261
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2368
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 131
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3404
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4514
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20993
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 103
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 266
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 1.25e1
  variant carriers: 0
num of homozygotes: 0
population: European (Finnish)
population: South Asian
population: European (Non-Finnish)
population: African
population: Other
population: Latino
population: East Asian
reference allele: C
site quality: MQRankSum
site quality: MQ
site quality: FS
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: VQSLOD
site quality: QD
site quality: BaseQRankSum

16-89614383-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614383
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614383
    reference: chr 16
allele count: 1
allele frequency: 8.312137383006666e-6
allele num: 120306
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.279-28C>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1553-28C>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*226-28C>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.98-28C>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.151-28C>G
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1313
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 466
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 768
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2382
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 580
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 492
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14938
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 266
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3892
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7844
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 360
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1056
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4970
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14368
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 677
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 352
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3395
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1702
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 807
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21120
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1531
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 108
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13955
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 191
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 70
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 95
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3404
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3284
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 47
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 234
  bin: 3.75e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: African
population: European (Finnish)
population: European (Non-Finnish)
population: Latino
population: Other
population: South Asian
reference allele: C
site quality: ClippingRankSum
site quality: DP
site quality: InbreedingCoeff
site quality: FS
site quality: QD
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: MQ
site quality: BaseQRankSum

16-89614383-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614383
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614383
    reference: chr 16
allele count: 2
allele frequency: 1.662427476601333e-5
allele num: 120306
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.279-28C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1553-28C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.98-28C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.151-28C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*226-28C>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 768
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 807
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1056
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3395
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 466
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 360
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7844
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 352
  bin: 8.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 3892
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14938
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4970
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14368
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1702
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2382
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 677
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1313
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 492
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 266
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 580
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 70
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 191
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13955
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 3404
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 47
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 245
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 95
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1531
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 632
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 108
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4515
  bin: 7.75e1
  variant carriers: 0
num of homozygotes: 0
population: European (Non-Finnish)
population: East Asian
population: Latino
population: European (Finnish)
population: South Asian
population: African
population: Other
reference allele: C
site quality: MQRankSum
site quality: BaseQRankSum
site quality: MQ
site quality: VQSLOD
site quality: FS
site quality: DP
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: ReadPosRankSum

16-89614385-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614385
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614385
    reference: chr 16
allele count: 17
allele frequency: 1.412992885165237e-4
allele num: 120312
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1553-26C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.98-26C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.151-26C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*226-26C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.279-26C>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 349
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4967
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1056
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 264
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 73
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14961
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 338
  bin: 1.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 3395
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 774
  bin: 9.75e1
  variant carriers: 13
genotype depth: GenotypeDepth
  all individuals: 644
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 465
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 492
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1311
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14378
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3930
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7840
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1702
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 578
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 806
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 56
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 622
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 210
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3285
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 188
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2369
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 24
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 98
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 89
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 27
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8832
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3402
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4518
  bin: 7.75e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: East Asian
population: South Asian
population: European (Finnish)
population: Latino
population: Other
population: European (Non-Finnish)
reference allele: C
site quality: MQ
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: DP
site quality: VQSLOD
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: FS
site quality: ReadPosRankSum

16-89614390-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614390
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614390
    reference: chr 16
allele count: 16
allele frequency: 1.329654622211881e-4
allele num: 120332
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.279-21C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1553-21C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*226-21C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.151-21C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.98-21C>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 458
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14993
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3393
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1056
  bin: 6.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 771
  bin: 9.75e1
  variant carriers: 12
genotype depth: GenotypeDepth
  all individuals: 1313
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 804
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7840
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4051
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2382
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 349
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 273
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 569
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 68
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 491
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 579
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14386
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1700
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4967
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21307
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 88
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 161
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2369
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4519
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3402
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8848
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 623
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1528
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 24
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 71
  bin: 4.25e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: Other
population: European (Finnish)
population: East Asian
population: European (Non-Finnish)
population: Latino
population: South Asian
reference allele: C
site quality: BaseQRankSum
site quality: VQSLOD
site quality: MQ
site quality: FS
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: DP

16-89614391-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614391
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614391
    reference: chr 16
allele count: 2
allele frequency: 1.662013030182157e-5
allele num: 120336
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.279-20G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1553-20G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*226-20G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.151-20G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.98-20G>A
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1701
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 491
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4968
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2383
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4059
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15019
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 580
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 453
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1312
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 349
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14391
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3393
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 760
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 7842
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 804
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1055
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 558
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 55
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8854
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 66
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1530
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 88
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 60
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 55
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 180
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2370
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 156
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 165
  bin: 3.75e1
  variant carriers: 0
num of homozygotes: 0
population: European (Finnish)
population: East Asian
population: South Asian
population: Other
population: Latino
population: African
population: European (Non-Finnish)
reference allele: G
site quality: FS
site quality: MQRankSum
site quality: BaseQRankSum
site quality: QD
site quality: DP
site quality: ClippingRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQ

16-89614395-CTGTT-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614395
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614391
    reference: chr 16
allele count: 1
allele frequency: 8.306061763875276e-6
allele num: 120394
alternate allele: C
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1553-12_1553-9delTTGT
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.98-12_98-9delTTGT
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*226-12_*226-9delTTGT
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.279-12_279-9delTTGT
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.151-12_151-9delTTGT
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: VQSRTrancheINDEL95.00to96.00
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 160
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 56
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1056
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7842
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3393
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 579
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 758
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 14397
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 441
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 446
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 491
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2383
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1701
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15081
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4225
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1312
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4968
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 349
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 804
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 603
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8878
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 128
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 54
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21630
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3405
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3290
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 130
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 103
  bin: 3.75e1
  variant carriers: 0
num of homozygotes: 0
population: South Asian
population: Latino
population: African
population: East Asian
population: European (Non-Finnish)
population: European (Finnish)
population: Other
reference allele: CTGTT
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: VQSLOD
site quality: BaseQRankSum
site quality: FS
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: QD
site quality: DP
site quality: MQ

16-89614399-TTG-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614399
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614397
    reference: chr 16
allele count: 42
allele frequency: 3.487850653556777e-4
allele num: 120418
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.98-8_98-7delGT
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.151-8_151-7delGT
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1553-8_1553-7delGT
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*226-8_*226-7delGT
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.279-8_279-7delGT
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3393
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 798
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4291
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1307
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 788
  bin: 9.75e1
  variant carriers: 39
genotype depth: GenotypeDepth
  all individuals: 2382
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 50
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4967
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1051
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 382
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1700
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 139
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 437
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15110
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 7842
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 346
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14397
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 574
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13928
  bin: 9.75e1
  variant carriers: 41
genotype quality: GenotypeQuality
  all individuals: 21693
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 48
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 101
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 124
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3402
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 38
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1528
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3286
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 48
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8881
  bin: 6.75e1
  variant carriers: 0
num of homozygotes: 1
population: South Asian
population: African
population: East Asian
population: European (Non-Finnish)
population: European (Finnish)
population: Latino
population: Other
reference allele: TTG
site quality: FS
site quality: InbreedingCoeff
site quality: DP
site quality: ClippingRankSum
site quality: MQRankSum
site quality: QD
site quality: BaseQRankSum
site quality: VQSLOD
site quality: MQ
site quality: ReadPosRankSum

16-89614400-T-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614400
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614400
    reference: chr 16
allele count: 1
allele frequency: 8.309512730173502e-6
allele num: 120344
alternate allele: G
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1553-11T>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.151-11T>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.98-11T>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*226-11T>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.279-11T>G
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4967
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 574
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14401
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1306
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7841
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15112
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1051
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 434
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 368
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 798
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4310
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 346
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 132
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3393
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 751
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1700
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3402
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 98
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 49
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 579
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4522
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 24
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3286
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 35
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 72
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 119
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 1.25e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: Other
population: African
population: South Asian
population: European (Finnish)
population: Latino
population: European (Non-Finnish)
reference allele: T
site quality: FS
site quality: ClippingRankSum
site quality: MQ
site quality: MQRankSum
site quality: BaseQRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: QD
site quality: DP

16-89614405-T-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614405
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614405
    reference: chr 16
allele count: 1
allele frequency: 8.303854649328218e-6
allele num: 120426
alternate allele: G
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1553-6T>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.98-6T>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.151-6T>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*226-6T>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.279-6T>G
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 434
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 749
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4230
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 346
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14439
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 354
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15173
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3397
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1701
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 151
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1052
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4972
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7847
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 798
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 574
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1307
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2382
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 49
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 89
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 127
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 60
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4529
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1528
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2369
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13897
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3292
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 1.75e1
  variant carriers: 0
hgvs: c.1553-6T>G
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: East Asian
population: South Asian
population: Latino
population: European (Finnish)
population: Other
reference allele: T
site quality: MQ
site quality: InbreedingCoeff
site quality: DP
site quality: BaseQRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: FS
site quality: ClippingRankSum
site quality: QD
site quality: ReadPosRankSum

16-89614408-CAG-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614408
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614406
    reference: chr 16
allele count: 4
allele frequency: 3.321155762205247e-5
allele num: 120440
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: splice_acceptor_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*226-2_*226-1delAG
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: splice_acceptor_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1553-2_1553-1delAG
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_acceptor_variant
  consequence: non_coding_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.279-2_279-1delAG
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_acceptor_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.98-2_98-1delAG
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: splice_acceptor_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.151-2_151-1delAG
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: splice acceptor
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 145
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 14424
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2382
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 343
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4972
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1701
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4251
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 574
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1053
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 749
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 428
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15193
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 7844
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3397
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 346
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 798
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1308
  bin: 6.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3407
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21666
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 48
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 58
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 112
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 85
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3292
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4530
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8893
  bin: 6.75e1
  variant carriers: 0
hgvs: c.1553-2_1553-1delAG
num of homozygotes: 0
population: European (Finnish)
population: Other
population: Latino
population: European (Non-Finnish)
population: South Asian
population: African
population: East Asian
reference allele: CAG
site quality: MQRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: DP
site quality: MQ
site quality: QD
site quality: InbreedingCoeff
site quality: FS
site quality: ReadPosRankSum
site quality: BaseQRankSum

16-89614418-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614418
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614418
    reference: chr 16
allele count: 2
allele frequency: 1.66024704476026e-5
allele num: 120464
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.286C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.158C>T
  hgvsp: ENST00000566221.1:c.158C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1560C>T
  hgvsp: ENST00000268704.2:c.1560C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.105C>T
  hgvsp: ENST00000561911.1:c.105C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*233C>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 419
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 139
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 751
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 347
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14412
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4266
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4972
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15205
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3397
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 260
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1307
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 574
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 798
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1701
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2382
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7843
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 346
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1051
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4528
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21745
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3295
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 580
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2366
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 68
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 110
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 80
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Asp520Asp
num of homozygotes: 0
population: Other
population: European (Non-Finnish)
population: African
population: East Asian
population: Latino
population: South Asian
population: European (Finnish)
reference allele: C
site quality: InbreedingCoeff
site quality: DP
site quality: VQSLOD
site quality: QD
site quality: ClippingRankSum
site quality: FS
site quality: MQRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQ

16-89614419-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614419
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614419
    reference: chr 16
allele count: 1
allele frequency: 8.301510874979247e-6
allele num: 120460
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.159A>G
  hgvsp: ENSP00000457298.1:p.Ile54Val
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.287A>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*234A>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1561A>G
  hgvsp: ENSP00000268704.2:p.Ile521Val
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.106A>G
  hgvsp: ENSP00000457387.1:p.Ile36Val
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 346
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 345
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4974
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 574
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1052
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15206
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 421
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 798
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 141
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4260
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14416
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7842
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3397
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 749
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1307
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 260
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1701
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2382
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21730
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3294
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2366
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8882
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 40
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 580
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1526
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4525
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 77
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Ile521Val
num of homozygotes: 0
population: South Asian
population: European (Non-Finnish)
population: European (Finnish)
population: African
population: Latino
population: East Asian
population: Other
reference allele: A
site quality: MQ
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: DP
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: MQRankSum
site quality: QD
site quality: FS
site quality: VQSLOD

16-89614421-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614421
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614421
    reference: chr 16
allele count: 2
allele frequency: 1.66024704476026e-5
allele num: 120464
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.108C>G
  hgvsp: ENSP00000457387.1:p.Ile36Met
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1563C>G
  hgvsp: ENSP00000268704.2:p.Ile521Met
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*236C>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.289C>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.161C>G
  hgvsp: ENSP00000457298.1:p.Ile54Met
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 14416
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1701
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 414
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3397
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1307
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2382
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4973
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1052
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7847
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 798
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 333
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4269
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 574
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 139
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 748
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 346
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15211
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 101
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4525
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 53
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8881
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1526
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3294
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21801
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 61
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 76
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Ile521Met
num of homozygotes: 0
population: European (Non-Finnish)
population: Latino
population: European (Finnish)
population: East Asian
population: Other
population: African
population: South Asian
reference allele: C
site quality: MQ
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: QD
site quality: VQSLOD
site quality: FS
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: DP

16-89614422-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614422
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614422
    reference: chr 16
allele count: 2
allele frequency: 1.660384877214538e-5
allele num: 120454
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1564G>A
  hgvsp: ENSP00000268704.2:p.Ala522Thr
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*237G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.109G>A
  hgvsp: ENSP00000457387.1:p.Ala37Thr
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.162G>A
  hgvsp: ENSP00000457298.1:p.Ala55Thr
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.290G>A
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 749
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1053
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 798
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 346
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4973
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 151
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4248
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 416
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15200
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 341
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1307
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1701
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14424
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3396
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 574
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7847
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 37
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 85
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13896
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2368
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 588
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3402
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 102
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 67
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21715
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Ala522Thr
num of homozygotes: 0
population: European (Non-Finnish)
population: Latino
population: East Asian
population: South Asian
population: African
population: European (Finnish)
population: Other
reference allele: G
site quality: MQRankSum
site quality: MQ
site quality: FS
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: DP
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: BaseQRankSum
site quality: QD

16-89614422-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614422
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614422
    reference: chr 16
allele count: 1
allele frequency: 8.301924386072691e-6
allele num: 120454
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.162G>T
  hgvsp: ENSP00000457298.1:p.Ala55Ser
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.109G>T
  hgvsp: ENSP00000457387.1:p.Ala37Ser
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1564G>T
  hgvsp: ENSP00000268704.2:p.Ala522Ser
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*237G>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.290G>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 14424
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 341
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 346
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 574
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4973
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15200
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4248
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1701
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3396
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 151
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 798
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 416
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 749
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1307
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7847
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1053
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 102
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 85
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 67
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 37
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 588
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3402
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 67
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3290
  bin: 7.25e1
  variant carriers: 0
hgvs: p.Ala522Ser
num of homozygotes: 0
population: European (Non-Finnish)
population: Latino
population: Other
population: South Asian
population: East Asian
population: European (Finnish)
population: African
reference allele: G
site quality: FS
site quality: VQSLOD
site quality: MQRankSum
site quality: DP
site quality: MQ
site quality: QD
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum

16-89614442-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614442
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614442
    reference: chr 16
allele count: 1
allele frequency: 8.311861025683651e-6
allele num: 120310
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.129T>C
  hgvsp: ENST00000561911.1:c.129T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.182T>C
  hgvsp: ENST00000566221.1:c.182T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*257T>C
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1584T>C
  hgvsp: ENST00000268704.2:c.1584T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.310T>C
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15178
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 56
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4974
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 574
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1052
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14427
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 479
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4065
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 406
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1701
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 219
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1306
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 798
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 748
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3396
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7846
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 346
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3402
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 115
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 62
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 682
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1527
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 69
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2367
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21496
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 111
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 74
  bin: 4.75e1
  variant carriers: 0
hgvs: p.Ala528Ala
num of homozygotes: 0
population: Latino
population: European (Non-Finnish)
population: South Asian
population: East Asian
population: African
population: European (Finnish)
population: Other
reference allele: T
site quality: ReadPosRankSum
site quality: MQ
site quality: MQRankSum
site quality: QD
site quality: FS
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: BaseQRankSum
site quality: DP

16-89614444-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614444
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614444
    reference: chr 16
allele count: 1
allele frequency: 8.313381218409152e-6
allele num: 120288
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*259C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.184C>T
  hgvsp: ENSP00000457298.1:p.Ala62Val
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.312C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1586C>T
  hgvsp: ENSP00000268704.2:p.Ala529Val
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.131C>T
  hgvsp: ENSP00000457387.1:p.Ala44Val
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 4973
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4038
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1052
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 491
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3396
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1306
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 574
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15147
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 346
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14438
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1701
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7845
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 748
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 238
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 422
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 797
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 64
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21435
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 133
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8857
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 53
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2368
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 705
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1527
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 123
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3284
  bin: 7.25e1
  variant carriers: 0
hgvs: p.Ala529Val
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: African
population: South Asian
population: Other
population: East Asian
population: European (Non-Finnish)
reference allele: C
site quality: MQ
site quality: ClippingRankSum
site quality: MQRankSum
site quality: FS
site quality: BaseQRankSum
site quality: VQSLOD
site quality: DP
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: QD

16-89614445-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614445
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614445
    reference: chr 16
allele count: 4
allele frequency: 3.326513979675e-5
allele num: 120246
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1587G>A
  hgvsp: ENST00000268704.2:c.1587G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.313G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.132G>A
  hgvsp: ENST00000561911.1:c.132G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.185G>A
  hgvsp: ENST00000566221.1:c.185G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*260G>A
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 7845
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15130
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 436
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 345
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 574
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4973
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4024
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 241
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 504
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1701
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14440
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1051
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3397
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 750
  bin: 9.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 797
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1305
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 66
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 124
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4519
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 56
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2368
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 96
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3280
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 715
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21370
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 69
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Ala529Ala
num of homozygotes: 0
population: East Asian
population: South Asian
population: African
population: Latino
population: European (Finnish)
population: Other
population: European (Non-Finnish)
reference allele: G
site quality: FS
site quality: ClippingRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: DP
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: QD
site quality: MQ

16-89614447-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614447
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614447
    reference: chr 16
allele count: 1
allele frequency: 8.315316813570598e-6
allele num: 120260
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*262T>C
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.187T>C
  hgvsp: ENSP00000457298.1:p.Leu63Pro
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1589T>C
  hgvsp: ENSP00000268704.2:p.Leu530Pro
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.315T>C
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.134T>C
  hgvsp: ENSP00000457387.1:p.Leu45Pro
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 14436
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4034
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 501
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3396
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4973
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 747
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1703
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 442
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15133
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1051
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 233
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1305
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 797
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7844
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 345
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 573
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 127
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 58
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 57
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 717
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21433
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3279
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 121
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13888
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 8847
  bin: 6.75e1
  variant carriers: 0
hgvs: p.Leu530Pro
num of homozygotes: 0
population: East Asian
population: Other
population: African
population: Latino
population: European (Non-Finnish)
population: European (Finnish)
population: South Asian
reference allele: T
site quality: VQSLOD
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: FS
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: DP
site quality: ReadPosRankSum
site quality: MQ

16-89614451-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614451
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614451
    reference: chr 16
allele count: 17
allele frequency: 1.414097722470844e-4
allele num: 120218
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.319C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*266C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.191C>T
  hgvsp: ENST00000566221.1:c.191C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.138C>T
  hgvsp: ENST00000561911.1:c.138C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1593C>T
  hgvsp: ENST00000268704.2:c.1593C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 481
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 260
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14440
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 344
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 523
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 233
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 757
  bin: 9.75e1
  variant carriers: 16
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4973
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15127
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3396
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 573
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 794
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7844
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3972
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1702
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1047
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1304
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2368
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1527
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 128
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 35
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8831
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 66
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 74
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3400
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 149
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 68
  bin: 5.25e1
  variant carriers: 0
hgvs: p.His531His
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: East Asian
population: South Asian
population: Latino
population: Other
population: European (Finnish)
reference allele: C
site quality: DP
site quality: FS
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: ClippingRankSum
site quality: QD
site quality: MQRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQ

16-89614452-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614452
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614452
    reference: chr 16
allele count: 1
allele frequency: 8.320713584396998e-6
allele num: 120182
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.139G>A
  hgvsp: ENSP00000457387.1:p.Ala47Thr
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1594G>A
  hgvsp: ENSP00000268704.2:p.Ala532Thr
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*267G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.192G>A
  hgvsp: ENSP00000457298.1:p.Ala65Thr
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.320G>A
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1303
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 344
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3946
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 64
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 526
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 238
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7844
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 573
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1702
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14446
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 499
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3397
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1047
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15131
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4974
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 260
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 795
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 742
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 755
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3277
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8832
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 75
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 55
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21362
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 35
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 130
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4513
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 69
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 35
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 143
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Ala532Thr
num of homozygotes: 0
population: East Asian
population: African
population: Latino
population: South Asian
population: Other
population: European (Finnish)
population: European (Non-Finnish)
reference allele: G
site quality: QD
site quality: FS
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: MQ
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: DP

16-89614454-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614454
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614454
    reference: chr 16
allele count: 5
allele frequency: 4.162088369460261e-5
allele num: 120132
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.322G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1596G>A
  hgvsp: ENST00000268704.2:c.1596G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*269G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.194G>A
  hgvsp: ENST00000566221.1:c.194G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.141G>A
  hgvsp: ENST00000561911.1:c.141G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3397
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 573
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1702
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7844
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 252
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 542
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 794
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 67
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 520
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 260
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4976
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3910
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15116
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1046
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 342
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 745
  bin: 9.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 1303
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14440
  bin: 3.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 53
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 785
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 104
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 155
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 144
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 123
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 74
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3276
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21269
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 69
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13872
  bin: 9.75e1
  variant carriers: 5
hgvs: p.Ala532Ala
num of homozygotes: 0
population: East Asian
population: Other
population: African
population: South Asian
population: European (Finnish)
population: European (Non-Finnish)
population: Latino
reference allele: G
site quality: FS
site quality: MQRankSum
site quality: BaseQRankSum
site quality: QD
site quality: VQSLOD
site quality: MQ
site quality: ReadPosRankSum
site quality: DP
site quality: InbreedingCoeff
site quality: ClippingRankSum

16-89614456-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614456
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614456
    reference: chr 16
allele count: 1
allele frequency: 8.324315325064513e-6
allele num: 120130
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.196C>T
  hgvsp: ENSP00000457298.1:p.Ala66Val
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1598C>T
  hgvsp: ENSP00000268704.2:p.Ala533Val
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.143C>T
  hgvsp: ENSP00000457387.1:p.Ala48Val
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*271C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.324C>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 4974
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 68
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 794
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 547
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3935
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14434
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 241
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 516
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1702
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3397
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2382
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1303
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15112
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7843
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 572
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 742
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1046
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 260
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 342
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3399
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2368
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3279
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1529
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21351
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 35
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 137
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 118
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 80
  bin: 5.25e1
  variant carriers: 0
hgvs: p.Ala533Val
num of homozygotes: 0
population: European (Finnish)
population: South Asian
population: African
population: Latino
population: European (Non-Finnish)
population: Other
population: East Asian
reference allele: C
site quality: QD
site quality: FS
site quality: BaseQRankSum
site quality: VQSLOD
site quality: DP
site quality: MQ
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: ClippingRankSum
site quality: ReadPosRankSum

16-89614457-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614457
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614457
    reference: chr 16
allele count: 3
allele frequency: 2.497544081653041e-5
allele num: 120118
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1599G>A
  hgvsp: ENST00000268704.2:c.1599G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.144G>A
  hgvsp: ENST00000561911.1:c.144G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.197G>A
  hgvsp: ENST00000566221.1:c.197G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.325G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*272G>A
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 260
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14433
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 519
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 572
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3396
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1302
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1046
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 794
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1702
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 230
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 552
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4974
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3946
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2382
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7842
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 743
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 342
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15106
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8819
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21375
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4513
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3278
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13867
  bin: 9.75e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 51
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 72
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2368
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 24
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 151
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 137
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 788
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Ala533Ala
num of homozygotes: 0
population: East Asian
population: South Asian
population: European (Non-Finnish)
population: African
population: European (Finnish)
population: Other
population: Latino
reference allele: G
site quality: VQSLOD
site quality: FS
site quality: InbreedingCoeff
site quality: MQ
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: QD
site quality: DP
site quality: ClippingRankSum

16-89614458-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614458
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614458
    reference: chr 16
allele count: 1
allele frequency: 8.32514693884347e-6
allele num: 120118
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1600C>T
  hgvsp: ENSP00000268704.2:p.Arg534Trp
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.198C>T
  hgvsp: ENSP00000457298.1:p.Arg67Trp
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.326C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.145C>T
  hgvsp: ENSP00000457387.1:p.Arg49Trp
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*273C>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 522
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14431
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 224
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1702
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2382
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4975
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 260
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 342
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15094
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 555
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 70
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 794
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3958
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7843
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 572
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 741
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1303
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1046
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 488
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3396
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 796
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 72
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 70
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 49
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 138
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 37
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4509
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 112
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21381
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 149
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8818
  bin: 6.75e1
  variant carriers: 0
hgvs: p.Arg534Trp
num of homozygotes: 0
population: European (Non-Finnish)
population: Other
population: African
population: South Asian
population: European (Finnish)
population: East Asian
population: Latino
reference allele: C
site quality: BaseQRankSum
site quality: MQRankSum
site quality: FS
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: DP
site quality: QD
site quality: MQ

16-89614459-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614459
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614459
    reference: chr 16
allele count: 12
allele frequency: 9.990675369654989e-5
allele num: 120112
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.327G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.146G>A
  hgvsp: ENSP00000457387.1:p.Arg49Gln
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1601G>A
  hgvsp: ENSP00000268704.2:p.Arg534Gln
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*274G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.199G>A
  hgvsp: ENSP00000457298.1:p.Arg67Gln
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 226
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1046
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1700
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14429
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2382
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 71
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 571
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1301
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3396
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3963
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 560
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15083
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7841
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 524
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 794
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 260
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 340
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4973
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 751
  bin: 9.75e1
  variant carriers: 10
genotype depth: GenotypeDepth
  all individuals: 487
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 71
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8817
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 112
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 72
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 150
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21391
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 66
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13865
  bin: 9.75e1
  variant carriers: 12
genotype quality: GenotypeQuality
  all individuals: 3275
  bin: 7.25e1
  variant carriers: 0
hgvs: p.Arg534Gln
num of homozygotes: 0
population: African
population: East Asian
population: European (Finnish)
population: European (Non-Finnish)
population: South Asian
population: Latino
population: Other
reference allele: G
site quality: BaseQRankSum
site quality: FS
site quality: MQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: DP
site quality: QD

16-89614465-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614465
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614465
    reference: chr 16
allele count: 1
allele frequency: 8.329723786359244e-6
allele num: 120052
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*280G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1607G>A
  hgvsp: ENSP00000268704.2:p.Gly536Glu
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.205G>A
  hgvsp: ENSP00000457298.1:p.Gly69Glu
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.333G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.152G>A
  hgvsp: ENSP00000457387.1:p.Gly51Glu
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2383
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1700
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 201
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3950
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7841
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14425
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 742
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 793
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1303
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 530
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4973
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15093
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 80
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1047
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 583
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 340
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3398
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 570
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 487
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8821
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 81
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1529
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3269
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2367
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 88
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 42
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 830
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 148
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Gly536Glu
num of homozygotes: 0
population: European (Finnish)
population: East Asian
population: Other
population: African
population: South Asian
population: European (Non-Finnish)
population: Latino
reference allele: G
site quality: DP
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: FS
site quality: BaseQRankSum
site quality: MQ
site quality: QD

16-89614465-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614465
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614465
    reference: chr 16
allele count: 1
allele frequency: 8.329723786359244e-6
allele num: 120052
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.333G>C
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1607G>C
  hgvsp: ENSP00000268704.2:p.Gly536Ala
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.152G>C
  hgvsp: ENSP00000457387.1:p.Gly51Ala
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.205G>C
  hgvsp: ENSP00000457298.1:p.Gly69Ala
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*280G>C
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 583
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 793
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 340
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4973
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15093
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1303
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3398
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 80
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7841
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2383
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14425
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 530
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 201
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 570
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 487
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1700
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1047
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 742
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3950
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 81
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2367
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 129
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3269
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13861
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 88
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21444
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 148
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8821
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 830
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 42
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Gly536Ala
num of homozygotes: 0
population: African
population: Latino
population: Other
population: South Asian
population: European (Finnish)
population: East Asian
population: European (Non-Finnish)
reference allele: G
site quality: VQSLOD
site quality: ClippingRankSum
site quality: FS
site quality: MQ
site quality: QD
site quality: DP
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff

16-89614468-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614468
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614468
    reference: chr 16
allele count: 2
allele frequency: 1.666583337499792e-5
allele num: 120006
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.208A>G
  hgvsp: ENSP00000457298.1:p.His70Arg
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.155A>G
  hgvsp: ENSP00000457387.1:p.His52Arg
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1610A>G
  hgvsp: ENSP00000268704.2:p.His537Arg
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*283A>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.336A>G
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 4973
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 793
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 88
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3928
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 597
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 742
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 7840
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3398
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1700
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14420
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1303
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 569
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1047
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 178
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 487
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15094
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 559
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 340
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 259
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2383
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 141
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2367
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 129
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 88
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 873
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3267
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13859
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 21438
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1529
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 38
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 56
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 2.5e0
  variant carriers: 0
hgvs: p.His537Arg
num of homozygotes: 0
population: Latino
population: Other
population: South Asian
population: African
population: European (Non-Finnish)
population: East Asian
population: European (Finnish)
reference allele: A
site quality: ReadPosRankSum
site quality: QD
site quality: MQ
site quality: DP
site quality: ClippingRankSum
site quality: VQSLOD
site quality: FS
site quality: MQRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff

16-89614469-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614469
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614469
    reference: chr 16
allele count: 12
allele frequency: 1.000300090027008e-4
allele num: 119964
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.156C>G
  hgvsp: ENSP00000457387.1:p.His52Gln
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1611C>G
  hgvsp: ENSP00000268704.2:p.His537Gln
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*284C>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.337C>G
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.209C>G
  hgvsp: ENSP00000457298.1:p.His70Gln
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 7839
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3897
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 568
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3399
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 190
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1047
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1698
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 484
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 793
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 90
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15077
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14423
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 610
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 751
  bin: 9.75e1
  variant carriers: 12
genotype depth: GenotypeDepth
  all individuals: 339
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4973
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1302
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 579
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 74
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 895
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 79
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 89
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 138
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 145
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 39
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2367
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3267
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4503
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8810
  bin: 6.75e1
  variant carriers: 0
hgvs: p.His537Gln
num of homozygotes: 0
population: Other
population: Latino
population: East Asian
population: African
population: European (Finnish)
population: European (Non-Finnish)
population: South Asian
reference allele: C
site quality: VQSLOD
site quality: DP
site quality: ClippingRankSum
site quality: QD
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: MQ

16-89614473-TC-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614473
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614472
    reference: chr 16
allele count: 2
allele frequency: 1.66741700431861e-5
allele num: 119946
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*290delC
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.215delC
  hgvsp: ENSP00000457298.1:p.Val73CysfsTer29
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: frameshift_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1617delC
  hgvsp: ENSP00000268704.2:p.Val540CysfsTer52
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.343delC
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.162delC
  hgvsp: ENSP00000457387.1:p.Val55CysfsTer52
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: frameshift
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1698
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14426
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 483
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3399
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15075
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 576
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 618
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7841
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 93
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3916
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 792
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 568
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 169
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 339
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1047
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1302
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4976
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 741
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 129
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3267
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 64
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 42
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 53
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13847
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 21432
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 911
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4501
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 143
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Val540CysfsTer52
num of homozygotes: 0
population: European (Non-Finnish)
population: African
population: European (Finnish)
population: Latino
population: Other
population: East Asian
population: South Asian
reference allele: TC
site quality: DP
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: MQRankSum
site quality: QD
site quality: FS
site quality: MQ
site quality: ReadPosRankSum
site quality: ClippingRankSum

16-89614475-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614475
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614475
    reference: chr 16
allele count: 2
allele frequency: 1.668168017882761e-5
allele num: 119892
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1617C>T
  hgvsp: ENST00000268704.2:c.1617C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.215C>T
  hgvsp: ENST00000566221.1:c.215C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.162C>T
  hgvsp: ENST00000561911.1:c.162C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*290C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.343C>T
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: synonymous
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 171
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1046
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1302
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3399
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 601
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1698
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 743
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 792
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 636
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14428
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 568
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15060
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3879
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 339
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7841
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 482
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4976
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 136
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4501
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 943
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 100
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3268
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21394
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8807
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 150
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Ser539Ser
num of homozygotes: 0
population: Other
population: South Asian
population: European (Finnish)
population: European (Non-Finnish)
population: African
population: East Asian
population: Latino
reference allele: C
site quality: DP
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: FS
site quality: QD
site quality: MQ
site quality: ClippingRankSum
site quality: MQRankSum
site quality: ReadPosRankSum

16-89614476-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614476
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614476
    reference: chr 16
allele count: 3
allele frequency: 2.502502502502503e-5
allele num: 119880
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.163G>A
  hgvsp: ENSP00000457387.1:p.Val55Met
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.344G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1618G>A
  hgvsp: ENSP00000268704.2:p.Val540Met
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*291G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.216G>A
  hgvsp: ENSP00000457298.1:p.Val73Met
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 339
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14429
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4976
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1046
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 158
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 600
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3399
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 567
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7843
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15063
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1698
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 640
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 792
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 482
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 741
  bin: 9.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1302
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3886
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1530
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21421
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 60
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 98
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3263
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4500
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 147
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8804
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 950
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Val540Met
num of homozygotes: 0
population: South Asian
population: Other
population: Latino
population: European (Finnish)
population: African
population: East Asian
population: European (Non-Finnish)
reference allele: G
site quality: FS
site quality: QD
site quality: DP
site quality: ClippingRankSum
site quality: MQ
site quality: VQSLOD
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: ReadPosRankSum

16-89614482-ACT-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614482
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614480
    reference: chr 16
allele count: 3
allele frequency: 2.505679540291327e-5
allele num: 119728
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.354_355delTC
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.226_227delTC
  hgvsp: ENSP00000457298.1:p.Leu76GlnfsTer134
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: frameshift_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1628_1629delTC
  hgvsp: ENSP00000268704.2:p.Leu543GlnfsTer32
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*301_*302delTC
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.173_174delTC
  hgvsp: ENSP00000457387.1:p.Leu58GlnfsTer32
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: frameshift
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 159
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1046
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3761
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 791
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 693
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 481
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14424
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7840
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15034
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 690
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1698
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 113
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3400
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 567
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 741
  bin: 9.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 4976
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1301
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 339
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3252
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3397
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 160
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 38
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 168
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1034
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 52
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 35
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1530
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 111
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Leu543GlnfsTer32
num of homozygotes: 0
population: South Asian
population: East Asian
population: European (Non-Finnish)
population: European (Finnish)
population: African
population: Latino
population: Other
reference allele: ACT
site quality: MQ
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: QD
site quality: MQRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: DP
site quality: ClippingRankSum

16-89614484-T-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614484
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614484
    reference: chr 16
allele count: 3
allele frequency: 2.506935855867901e-5
allele num: 119668
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.352T>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*299T>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.171T>A
  hgvsp: ENST00000561911.1:c.171T>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1626T>A
  hgvsp: ENST00000268704.2:c.1626T>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.224T>A
  hgvsp: ENST00000566221.1:c.224T>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3400
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1046
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7840
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 257
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1698
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 724
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4976
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 481
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 725
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 171
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 742
  bin: 9.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 15012
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3703
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 338
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 116
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 791
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1301
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14423
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 566
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 60
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 118
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 27
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1530
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3251
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4494
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2366
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 176
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1098
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Thr542Thr
num of homozygotes: 0
population: Latino
population: African
population: East Asian
population: European (Finnish)
population: European (Non-Finnish)
population: Other
population: South Asian
reference allele: T
site quality: MQ
site quality: InbreedingCoeff
site quality: DP
site quality: VQSLOD
site quality: ClippingRankSum
site quality: QD
site quality: MQRankSum
site quality: FS
site quality: ReadPosRankSum
site quality: BaseQRankSum

http://identifiers.org/exac.variant/16-89614487-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614487
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614487
    reference: chr 16
allele count: 1
allele frequency: 8.360784576024614e-6
allele num: 119606
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.174C>A
  hgvsp: ENST00000561911.1:c.174C>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.355C>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.227C>A
  hgvsp: ENST00000566221.1:c.227C>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*302C>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1629C>A
  hgvsp: ENST00000268704.2:c.1629C>A(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 766
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1698
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4976
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 131
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3400
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3626
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 184
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14998
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1301
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 481
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14426
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 747
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 738
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1046
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7842
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 566
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 791
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 338
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 184
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 198
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 37
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1530
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1139
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 128
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 43
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2366
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4495
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3247
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Leu543Leu
num of homozygotes: 0
population: East Asian
population: Latino
population: Other
population: European (Non-Finnish)
population: European (Finnish)
population: South Asian
population: African
reference allele: C
site quality: FS
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQ
site quality: MQRankSum
site quality: DP
site quality: QD

16-89614493-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614493
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614493
    reference: chr 16
allele count: 4
allele frequency: 3.352329869259135e-5
allele num: 119320
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.180C>T
  hgvsp: ENST00000561911.1:c.180C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*308C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.361C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1635C>T
  hgvsp: ENST00000268704.2:c.1635C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.233C>T
  hgvsp: ENST00000566221.1:c.233C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 879
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14867
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 741
  bin: 9.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 1698
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3400
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14408
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 855
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 480
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4976
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1301
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 245
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 790
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7842
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3461
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1046
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 338
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 256
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 566
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 165
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8735
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20809
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1529
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 72
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1283
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4487
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 229
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 57
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 64
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Phe545Phe
num of homozygotes: 0
population: South Asian
population: Other
population: East Asian
population: European (Finnish)
population: African
population: Latino
population: European (Non-Finnish)
reference allele: C
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQ
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: QD
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: FS
site quality: DP

16-89614494-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614494
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614494
    reference: chr 16
allele count: 1
allele frequency: 8.381386616601851e-6
allele num: 119312
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1636G>A
  hgvsp: ENSP00000268704.2:p.Glu546Lys
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.234G>A
  hgvsp: ENSP00000457298.1:p.Glu79Lys
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.181G>A
  hgvsp: ENSP00000457387.1:p.Glu61Lys
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*309G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.362G>A
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3460
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1046
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4976
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 863
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14873
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 160
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 480
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 566
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 338
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 238
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1698
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 880
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3400
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 256
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1301
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 790
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14409
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7840
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 736
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 206
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13831
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1529
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 53
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 35
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20858
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 87
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 54
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 164
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1296
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 52
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 5.75e1
  variant carriers: 0
hgvs: p.Glu546Lys
num of homozygotes: 0
population: European (Finnish)
population: Latino
population: East Asian
population: European (Non-Finnish)
population: Other
population: African
population: South Asian
reference allele: G
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: BaseQRankSum
site quality: MQ
site quality: FS
site quality: QD
site quality: MQRankSum
site quality: ClippingRankSum
site quality: DP

16-89614499-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614499
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614499
    reference: chr 16
allele count: 1
allele frequency: 8.404915194405689e-6
allele num: 118978
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.367C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.186C>T
  hgvsp: ENST00000561911.1:c.186C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*314C>T
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1641C>T
  hgvsp: ENST00000268704.2:c.1641C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.239C>T
  hgvsp: ENST00000566221.1:c.239C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1300
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3257
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 789
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1074
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 256
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 971
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14388
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4974
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1698
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1045
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7853
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 293
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14693
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 566
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 199
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 480
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3399
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 338
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 736
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1484
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 55
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 280
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3227
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4479
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 65
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 213
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 119
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13829
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 101
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8668
  bin: 6.75e1
  variant carriers: 0
hgvs: p.Tyr547Tyr
num of homozygotes: 0
population: East Asian
population: European (Non-Finnish)
population: African
population: Latino
population: Other
population: European (Finnish)
population: South Asian
reference allele: C
site quality: VQSLOD
site quality: MQRankSum
site quality: FS
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: QD
site quality: BaseQRankSum
site quality: MQ
site quality: DP
site quality: InbreedingCoeff

16-89614500-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 89614500
    reference: chr 16
  end: Position
    type: ExactPosition
    position: 89614500
    reference: chr 16
allele count: 3
allele frequency: 2.521898485179643e-5
allele num: 118958
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000268704
  ensembl transcript: ENST00000268704
  gene symbol: SPG7
  hgvsc: ENST00000268704.2:c.1642G>A
  hgvsp: ENSP00000268704.2:p.Ala548Thr
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457298
  ensembl transcript: ENST00000566221
  gene symbol: SPG7
  hgvsc: ENST00000566221.1:c.240G>A
  hgvsp: ENSP00000457298.1:p.Ala81Thr
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000454805
  ensembl transcript: ENST00000569820
  gene symbol: SPG7
  hgvsc: ENST00000569820.1:c.*315G>A
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000197912
  ensembl protein: ENSP00000457387
  ensembl transcript: ENST00000561911
  gene symbol: SPG7
  hgvsc: ENST00000561911.1:c.187G>A
  hgvsp: ENSP00000457387.1:p.Ala63Thr
  variant of: http://identifiers.org/hgnc/11237
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000197912
  ensembl transcript: ENST00000563218
  gene symbol: SPG7
  hgvsc: ENST00000563218.1:n.368G>A
  variant of: http://identifiers.org/hgnc/11237
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 7846
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14387
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4974
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3399
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 976
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14691
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 199
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 789
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2381
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 481
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 737
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1698
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1073
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 287
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 256
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1299
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3270
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1044
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 565
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 338
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 59
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 210
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 58
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13828
  bin: 9.75e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 20419
  bin: 6.25e1
  variant carriers: 0
hgvs: p.Ala548Thr
num of homozygotes: 0
reference allele: G

GenotypeQuality
all individuals: 3548
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 71
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 30
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 26
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3349
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 35043
bin: 9.75e1
variant carriers: 1

East Asian
type: Population
allele count: 1
allele frequency: 1.158211721102618e-4
allele num: 8634
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 1
allele frequency: 1.515151515151515e-4
allele num: 6600
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11568
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10398
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66550
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 2.24709e2

DP
type: SiteQuality
SIO_000300: 3.535111e6

BaseQRankSum
type: SiteQuality
SIO_000300: -3.198e0

MQRankSum
type: SiteQuality
SIO_000300: 1.09e0

MQ
type: SiteQuality
SIO_000300: 5.787e1

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.853e0

VQSLOD
type: SiteQuality
SIO_000300: -2.381e2

QD
type: SiteQuality
SIO_000300: 1.37e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.0e-4

ClippingRankSum
type: SiteQuality
SIO_000300: 2.38e0

GenotypeQuality
all individuals: 1829
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 7326
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 52
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3506
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2921
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3327
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 34
bin: 4.75e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11574
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 878
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10402
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5538
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.504257047444267e-5
allele num: 66478
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 9.442100000000001e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.429999999999999e-1

QD
type: SiteQuality
SIO_000300: 1.89e0

MQRankSum
type: SiteQuality
SIO_000300: 6.909999999999999e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.389e0

VQSLOD
type: SiteQuality
SIO_000300: -4.167e1

MQ
type: SiteQuality
SIO_000300: 5.604e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.5e-3

DP
type: SiteQuality
SIO_000300: 3.536077e6

BaseQRankSum
type: SiteQuality
SIO_000300: -3.857e0

GenotypeQuality
all individuals: 594
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 82
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1829
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3506
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2125
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2921
bin: 9.25e1
variant carriers: 1

GenotypeQuality
all individuals: 57
bin: 3.75e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10402
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11574
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 878
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 6
allele frequency: 1.083423618634886e-3
allele num: 5538
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.504257047444267e-5
allele num: 66478
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -4.167e1

FS
type: SiteQuality
SIO_000300: 9.442100000000001e1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.389e0

MQ
type: SiteQuality
SIO_000300: 5.604e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.5e-3

DP
type: SiteQuality
SIO_000300: 3.536077e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.429999999999999e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -3.857e0

MQRankSum
type: SiteQuality
SIO_000300: 6.909999999999999e-1

QD
type: SiteQuality
SIO_000300: 1.89e0

GenotypeQuality
all individuals: 1
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 19
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 0
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 7586
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 14
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1862
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3374
bin: 8.25e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11576
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8652
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66678
num of homozygotes: 0

South Asian
type: Population
allele count: 2
allele frequency: 1.211240310077519e-4
allele num: 16512
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.804e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.27e-1

FS
type: SiteQuality
SIO_000300: 3.264e0

VQSLOD
type: SiteQuality
SIO_000300: 7.61e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

DP
type: SiteQuality
SIO_000300: 3.50543e6

MQRankSum
type: SiteQuality
SIO_000300: 3.23e-1

QD
type: SiteQuality
SIO_000300: 1.31e1

ClippingRankSum
type: SiteQuality
SIO_000300: -7.29e-1

MQ
type: SiteQuality
SIO_000300: 5.933e1

GenotypeQuality
all individuals: 52
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 20
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4180
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1862
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 11
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3375
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2964
bin: 9.25e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66678
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8652
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.638562543192812e-5
allele num: 11576
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 9.640000000000001e0

FS
type: SiteQuality
SIO_000300: 2.687e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.24e0

ClippingRankSum
type: SiteQuality
SIO_000300: -4.86e-1

MQRankSum
type: SiteQuality
SIO_000300: -7.48e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

DP
type: SiteQuality
SIO_000300: 3.50538e6

BaseQRankSum
type: SiteQuality
SIO_000300: -4.868e0

VQSLOD
type: SiteQuality
SIO_000300: -2.096e0

MQ
type: SiteQuality
SIO_000300: 5.796e1

GenotypeQuality
all individuals: 0
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 14
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 19
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4181
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 9
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2180
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3377
bin: 8.25e1
variant carriers: 0

African
type: Population
allele count: 1
allele frequency: 9.611687812379854e-5
allele num: 10404
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66678
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11576
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.909e1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.263e0

VQSLOD
type: SiteQuality
SIO_000300: -1.91e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.725e0

QD
type: SiteQuality
SIO_000300: 1.482e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.16e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

MQRankSum
type: SiteQuality
SIO_000300: 2.06e-1

FS
type: SiteQuality
SIO_000300: 1.5328e1

DP
type: SiteQuality
SIO_000300: 3.505358e6

GenotypeQuality
all individuals: 4
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 0
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3376
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 0
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 24
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1862
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4
bin: 4.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8652
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.499520153550864e-5
allele num: 66688
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11576
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.0e-4

MQRankSum
type: SiteQuality
SIO_000300: 1.79e-1

MQ
type: SiteQuality
SIO_000300: 5.878e1

FS
type: SiteQuality
SIO_000300: 8.04e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.355e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.88e-1

VQSLOD
type: SiteQuality
SIO_000300: -6.666e-1

DP
type: SiteQuality
SIO_000300: 3.505485e6

ClippingRankSum
type: SiteQuality
SIO_000300: 9.25e-1

QD
type: SiteQuality
SIO_000300: 9.970000000000001e0

GenotypeQuality
all individuals: 4186
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 12
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 5
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 15
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 43
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2966
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2181
bin: 7.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11576
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.611687812379854e-5
allele num: 10404
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66688
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8652
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.75e1

MQRankSum
type: SiteQuality
SIO_000300: 1.38e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.43e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.0e-2

DP
type: SiteQuality
SIO_000300: 3.505559e6

VQSLOD
type: SiteQuality
SIO_000300: -2.966e-1

FS
type: SiteQuality
SIO_000300: 3.61e0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.898e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

MQ
type: SiteQuality
SIO_000300: 5.699e1

GenotypeQuality
all individuals: 3410
bin: 7.75e1
variant carriers: 2

GenotypeQuality
all individuals: 2031
bin: 7.25e1
variant carriers: 2

GenotypeQuality
all individuals: 5
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 1
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 17
bin: 5.25e1
variant carriers: 2

GenotypeQuality
all individuals: 3209
bin: 8.25e1
variant carriers: 5

GenotypeQuality
all individuals: 4002
bin: 6.75e1
variant carriers: 1

GenotypeQuality
all individuals: 36105
bin: 9.75e1
variant carriers: 16690

European (Non-Finnish)
type: Population
allele count: 12607
allele frequency: 1.890104947526237e-1
allele num: 66700
num of homozygotes: 1210

Other
type: Population
allele count: 152
allele frequency: 1.674008810572687e-1
allele num: 908
num of homozygotes: 14

South Asian
type: Population
allele count: 2234
allele frequency: 1.352955426356589e-1
allele num: 16512
num of homozygotes: 154

East Asian
type: Population
allele count: 1278
allele frequency: 1.478140180430257e-1
allele num: 8646
num of homozygotes: 98

African
type: Population
allele count: 358
allele frequency: 3.440984236831988e-2
allele num: 10404
num of homozygotes: 7

European (Finnish)
type: Population
allele count: 608
allele frequency: 9.192621711521017e-2
allele num: 6614
num of homozygotes: 27

Latino
type: Population
allele count: 1053
allele frequency: 9.099550639474593e-2
allele num: 11572
num of homozygotes: 61

BaseQRankSum
type: SiteQuality
SIO_000300: 3.06e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.49e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -3.4e-1

MQ
type: SiteQuality
SIO_000300: 5.875e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 2.54e-2

DP
type: SiteQuality
SIO_000300: 4.156756e6

QD
type: SiteQuality
SIO_000300: 1.424e1

MQRankSum
type: SiteQuality
SIO_000300: 2.48e-1

VQSLOD
type: SiteQuality
SIO_000300: 1.98e0

FS
type: SiteQuality
SIO_000300: 1.973e0

GenotypeQuality
all individuals: 13
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4413
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 11187
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3795
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 0
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4743
bin: 7.75e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11572
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8652
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10402
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.499295331194339e-5
allele num: 66698
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 2.597989e6

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

VQSLOD
type: SiteQuality
SIO_000300: -4.006e0

FS
type: SiteQuality
SIO_000300: 0.0e0

MQRankSum
type: SiteQuality
SIO_000300: 5.44e-1

MQ
type: SiteQuality
SIO_000300: 5.843e1

ClippingRankSum
type: SiteQuality
SIO_000300: -2.993e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.47e0

BaseQRankSum
type: SiteQuality
SIO_000300: 4.82e0

QD
type: SiteQuality
SIO_000300: 4.74e0

GenotypeQuality
all individuals: 18
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2876
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 15
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3794
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 19
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 10
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 11189
bin: 6.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8652
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.49934029027228e-5
allele num: 66696
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11572
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10402
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 5.695e0

MQ
type: SiteQuality
SIO_000300: 5.941e1

MQRankSum
type: SiteQuality
SIO_000300: -1.08e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -4.09e-1

QD
type: SiteQuality
SIO_000300: 2.011e1

DP
type: SiteQuality
SIO_000300: 2.597816e6

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.02e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 2.25e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

VQSLOD
type: SiteQuality
SIO_000300: -1.531e0

GenotypeQuality
all individuals: 4412
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 26
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 25356
bin: 9.75e1
variant carriers: 6

GenotypeQuality
all individuals: 3794
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 11205
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 15
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 5
bin: 4.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11572
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

South Asian
type: Population
allele count: 6
allele frequency: 3.633720930232558e-4
allele num: 16512
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66694
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8652
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10402
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.084e0

FS
type: SiteQuality
SIO_000300: 1.0404e1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.7e-1

MQRankSum
type: SiteQuality
SIO_000300: 4.83e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

VQSLOD
type: SiteQuality
SIO_000300: -1.448e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.34e-1

DP
type: SiteQuality
SIO_000300: 2.598007e6

QD
type: SiteQuality
SIO_000300: 1.274e1

MQ
type: SiteQuality
SIO_000300: 5.879e1

GenotypeQuality
all individuals: 4413
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 0
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 12
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4743
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 9
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2875
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 24
bin: 2.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 3
allele frequency: 4.498560460652591e-5
allele num: 66688
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

South Asian
type: Population
allele count: 2
allele frequency: 1.211240310077519e-4
allele num: 16512
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.155802126675913e-4
allele num: 8652
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.641548565502938e-5
allele num: 11572
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10402
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -6.2e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

VQSLOD
type: SiteQuality
SIO_000300: -6.102e-1

DP
type: SiteQuality
SIO_000300: 2.597639e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 8.01e-1

MQRankSum
type: SiteQuality
SIO_000300: 8.599999999999999e-2

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

MQ
type: SiteQuality
SIO_000300: 5.827e1

QD
type: SiteQuality
SIO_000300: 1.256e1

BaseQRankSum
type: SiteQuality
SIO_000300: -3.276e0

GenotypeQuality
all individuals: 22
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2872
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 56
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 25376
bin: 9.75e1
variant carriers: 304

GenotypeQuality
all individuals: 2304
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 15
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 5861
bin: 6.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8652
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 5
allele frequency: 7.559721802237678e-4
allele num: 6614
num of homozygotes: 0

South Asian
type: Population
allele count: 12
allele frequency: 7.267441860465116e-4
allele num: 16512
num of homozygotes: 1

European (Non-Finnish)
type: Population
allele count: 267
allele frequency: 4.003718809980806e-3
allele num: 66688
num of homozygotes: 1

Other
type: Population
allele count: 2
allele frequency: 2.202643171806168e-3
allele num: 908
num of homozygotes: 0

African
type: Population
allele count: 9
allele frequency: 8.652182272639877e-4
allele num: 10402
num of homozygotes: 0

Latino
type: Population
allele count: 11
allele frequency: 9.505703422053232e-4
allele num: 11572
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.888e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.8e-1

MQRankSum
type: SiteQuality
SIO_000300: 5.09e-1

FS
type: SiteQuality
SIO_000300: 1.349e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 8.500000000000001e-3

VQSLOD
type: SiteQuality
SIO_000300: 1.54e0

DP
type: SiteQuality
SIO_000300: 2.610819e6

QD
type: SiteQuality
SIO_000300: 1.285e1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.79e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -4.448e0

GenotypeQuality
all individuals: 7
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 14
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4432
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 15
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4758
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 25201
bin: 9.75e1
variant carriers: 2

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11572
num of homozygotes: 0

East Asian
type: Population
allele count: 2
allele frequency: 2.312138728323699e-4
allele num: 8650
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66662
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10398
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.979e1

QD
type: SiteQuality
SIO_000300: 1.508e1

VQSLOD
type: SiteQuality
SIO_000300: 2.38e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

BaseQRankSum
type: SiteQuality
SIO_000300: -6.507e0

ClippingRankSum
type: SiteQuality
SIO_000300: 2.36e-1

MQRankSum
type: SiteQuality
SIO_000300: 1.52e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.89e-1

FS
type: SiteQuality
SIO_000300: 8.7e-1

DP
type: SiteQuality
SIO_000300: 2.585556e6

GenotypeQuality
all individuals: 2
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 34
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 7
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 3809
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 25199
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 13
bin: 5.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11570
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.056201550387597e-5
allele num: 16512
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66660
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10398
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 1.364e0

VQSLOD
type: SiteQuality
SIO_000300: -1.324e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.6e-1

DP
type: SiteQuality
SIO_000300: 2.585272e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 8.36e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 6.24e0

MQRankSum
type: SiteQuality
SIO_000300: -6.8e-1

QD
type: SiteQuality
SIO_000300: 1.47e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

MQ
type: SiteQuality
SIO_000300: 5.877e1

GenotypeQuality
all individuals: 25198
bin: 9.75e1
variant carriers: 4

GenotypeQuality
all individuals: 117
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2877
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2312
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4755
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 7
bin: 4.75e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11566
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 4
allele frequency: 6.001860576778802e-5
allele num: 66646
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 904
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10394
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 9.58e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.7e0

ClippingRankSum
type: SiteQuality
SIO_000300: -3.94e-1

VQSLOD
type: SiteQuality
SIO_000300: 5.9e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.0e-4

BaseQRankSum
type: SiteQuality
SIO_000300: 3.78e-1

FS
type: SiteQuality
SIO_000300: 3.072e0

MQ
type: SiteQuality
SIO_000300: 5.908e1

DP
type: SiteQuality
SIO_000300: 2.584554e6

QD
type: SiteQuality
SIO_000300: 1.535e1

GenotypeQuality
all individuals: 7
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4753
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 57
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 5862
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 9
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3811
bin: 9.25e1
variant carriers: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.15606936416185e-4
allele num: 8650
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10394
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66640
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11568
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 5.65e0

VQSLOD
type: SiteQuality
SIO_000300: 1.38e0

BaseQRankSum
type: SiteQuality
SIO_000300: 1.03e0

DP
type: SiteQuality
SIO_000300: 2.584071e6

MQRankSum
type: SiteQuality
SIO_000300: -6.049e0

MQ
type: SiteQuality
SIO_000300: 5.179e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: 8.54e-1

FS
type: SiteQuality
SIO_000300: 1.935e0

ClippingRankSum
type: SiteQuality
SIO_000300: -8.27e-1

GenotypeQuality
all individuals: 4428
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 14
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 38
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2312
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 25194
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 52
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 11109
bin: 6.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11566
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66638
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.620935154897056e-5
allele num: 10394
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 904
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: -3.108e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

ClippingRankSum
type: SiteQuality
SIO_000300: -6.66e-1

QD
type: SiteQuality
SIO_000300: 1.237e1

MQRankSum
type: SiteQuality
SIO_000300: 2.51e0

FS
type: SiteQuality
SIO_000300: 1.198e0

VQSLOD
type: SiteQuality
SIO_000300: -1.873e0

DP
type: SiteQuality
SIO_000300: 2.583508e6

MQ
type: SiteQuality
SIO_000300: 5.772e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.68e-1

GenotypeQuality
all individuals: 2
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 11124
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 10
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2875
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 137
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2313
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 51
bin: 2.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11564
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10394
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.001290554938624e-5
allele num: 66638
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 1.23e0

FS
type: SiteQuality
SIO_000300: 4.657e0

VQSLOD
type: SiteQuality
SIO_000300: -5.286e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 2.27e-1

MQ
type: SiteQuality
SIO_000300: 5.875e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

DP
type: SiteQuality
SIO_000300: 2.583416e6

BaseQRankSum
type: SiteQuality
SIO_000300: 1.86e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.37e0

QD
type: SiteQuality
SIO_000300: 1.567e1

GenotypeQuality
all individuals: 25193
bin: 9.75e1
variant carriers: 4

GenotypeQuality
all individuals: 15
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4751
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3811
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2313
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 11059
bin: 6.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10392
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 4
allele frequency: 6.003662233962717e-5
allele num: 66626
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 904
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.999999999999999e-4

QD
type: SiteQuality
SIO_000300: 1.391e1

MQRankSum
type: SiteQuality
SIO_000300: -1.51e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -9.1e-1

MQ
type: SiteQuality
SIO_000300: 5.937e1

ClippingRankSum
type: SiteQuality
SIO_000300: -6.57e-1

VQSLOD
type: SiteQuality
SIO_000300: 5.49e-1

FS
type: SiteQuality
SIO_000300: 2.892e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.54e0

DP
type: SiteQuality
SIO_000300: 2.582652e6

GenotypeQuality
all individuals: 18
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 46
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 11014
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 86
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4755
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 5846
bin: 6.75e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10390
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66618
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.156604210039325e-4
allele num: 8646
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 904
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 3.422e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 8.22e-1

MQ
type: SiteQuality
SIO_000300: 5.909e1

VQSLOD
type: SiteQuality
SIO_000300: -8.794999999999999e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 5.02e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.209e0

MQRankSum
type: SiteQuality
SIO_000300: 1.25e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 9.0e-4

DP
type: SiteQuality
SIO_000300: 2.581757e6

QD
type: SiteQuality
SIO_000300: 7.73e0

GenotypeQuality
all individuals: 7
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 5830
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 32
bin: 4.75e1
variant carriers: 1

GenotypeQuality
all individuals: 25169
bin: 9.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4743
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3807
bin: 9.25e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6606
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11556
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 5
allele frequency: 7.509311546317433e-5
allele num: 66584
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10390
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8638
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -7.079e-1

MQRankSum
type: SiteQuality
SIO_000300: 5.5e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -3.24e-1

MQ
type: SiteQuality
SIO_000300: 5.863e1

QD
type: SiteQuality
SIO_000300: 6.23e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.79e-1

FS
type: SiteQuality
SIO_000300: 2.754e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 8.0e-4

BaseQRankSum
type: SiteQuality
SIO_000300: 4.42e-1

DP
type: SiteQuality
SIO_000300: 2.580245e6

GenotypeQuality
all individuals: 32
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 5
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 18
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3807
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2309
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4419
bin: 8.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11556
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.003724618526973e-5
allele num: 66584
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10390
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6606
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8638
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -3.24e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.79e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 8.0e-4

BaseQRankSum
type: SiteQuality
SIO_000300: 4.42e-1

FS
type: SiteQuality
SIO_000300: 2.754e0

QD
type: SiteQuality
SIO_000300: 6.23e0

VQSLOD
type: SiteQuality
SIO_000300: -7.079e-1

MQ
type: SiteQuality
SIO_000300: 5.863e1

MQRankSum
type: SiteQuality
SIO_000300: 5.5e-1

DP
type: SiteQuality
SIO_000300: 2.580245e6

GenotypeQuality
all individuals: 3
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 53
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2837
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 38
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4712
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 25164
bin: 9.75e1
variant carriers: 3

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8626
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11556
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10388
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 3
allele frequency: 4.506940688660537e-5
allele num: 66564
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 904
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -4.52e-1

MQ
type: SiteQuality
SIO_000300: 5.881e1

MQRankSum
type: SiteQuality
SIO_000300: -3.49e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.19e-1

VQSLOD
type: SiteQuality
SIO_000300: -2.798e-1

FS
type: SiteQuality
SIO_000300: 1.86e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.0e-4

DP
type: SiteQuality
SIO_000300: 2.576629e6

QD
type: SiteQuality
SIO_000300: 1.305e1

BaseQRankSum
type: SiteQuality
SIO_000300: -3.693e0

GenotypeQuality
all individuals: 440
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 57
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4396
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2299
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3796
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 5708
bin: 6.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11552
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10390
num of homozygotes: 0

South Asian
type: Population
allele count: 4
allele frequency: 2.422480620155039e-4
allele num: 16512
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8592
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66524
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.323e1

BaseQRankSum
type: SiteQuality
SIO_000300: -5.136e0

MQRankSum
type: SiteQuality
SIO_000300: 5.98e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 2.21e-1

VQSLOD
type: SiteQuality
SIO_000300: 8.32e-1

DP
type: SiteQuality
SIO_000300: 2.568826e6

MQ
type: SiteQuality
SIO_000300: 5.93e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.0e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: -5.2e-2

FS
type: SiteQuality
SIO_000300: 1.644e0

GenotypeQuality
all individuals: 58
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4397
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2299
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 25152
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 4703
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 37
bin: 5.75e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10390
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.164144353899884e-4
allele num: 8590
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66516
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11552
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 0.0e0

VQSLOD
type: SiteQuality
SIO_000300: -1.277e0

MQ
type: SiteQuality
SIO_000300: 5.726e1

QD
type: SiteQuality
SIO_000300: 1.648e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.0e-4

ClippingRankSum
type: SiteQuality
SIO_000300: 6.53e-1

DP
type: SiteQuality
SIO_000300: 2.567197e6

BaseQRankSum
type: SiteQuality
SIO_000300: 3.85e0

MQRankSum
type: SiteQuality
SIO_000300: 1.45e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.25e-1

GenotypeQuality
all individuals: 4386
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 254
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4679
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 102
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3790
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2296
bin: 8.75e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10384
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.056201550387597e-5
allele num: 16512
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.656509695290859e-5
allele num: 11552
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.50407604608489e-5
allele num: 66486
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8586
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -4.65e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

MQ
type: SiteQuality
SIO_000300: 5.852e1

MQRankSum
type: SiteQuality
SIO_000300: 3.25e-1

DP
type: SiteQuality
SIO_000300: 2.559638e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.3e-1

FS
type: SiteQuality
SIO_000300: 1.384e0

BaseQRankSum
type: SiteQuality
SIO_000300: -3.136e0

VQSLOD
type: SiteQuality
SIO_000300: -1.546e-1

QD
type: SiteQuality
SIO_000300: 1.207e1

GenotypeQuality
all individuals: 634
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 223
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4643
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 107
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4365
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3783
bin: 9.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8586
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10384
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6606
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 904
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 7
allele frequency: 1.053296819043606e-4
allele num: 66458
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11550
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.05e0

FS
type: SiteQuality
SIO_000300: 2.077e0

VQSLOD
type: SiteQuality
SIO_000300: 1.7e0

ClippingRankSum
type: SiteQuality
SIO_000300: 9.4e-2

BaseQRankSum
type: SiteQuality
SIO_000300: -2.737e0

MQ
type: SiteQuality
SIO_000300: 5.936e1

MQRankSum
type: SiteQuality
SIO_000300: -1.9e-2

InbreedingCoeff
type: SiteQuality
SIO_000300: 4.0e-4

DP
type: SiteQuality
SIO_000300: 2.548893e6

QD
type: SiteQuality
SIO_000300: 1.302e1

GenotypeQuality
all individuals: 4532
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2669
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4329
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3773
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 25113
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 985
bin: 3.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66368
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6596
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11534
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.63948332369385e-5
allele num: 10374
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 904
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8558
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -1.86e0

MQRankSum
type: SiteQuality
SIO_000300: 1.72e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.97e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 4.6e-3

QD
type: SiteQuality
SIO_000300: 5.98e0

ClippingRankSum
type: SiteQuality
SIO_000300: -5.4e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -3.215e0

FS
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 2.523554e6

GenotypeQuality
all individuals: 1691
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3733
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 25357
bin: 9.75e1
variant carriers: 388

GenotypeQuality
all individuals: 1094
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4270
bin: 8.25e1
variant carriers: 2

GenotypeQuality
all individuals: 2259
bin: 8.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6586
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 4
allele frequency: 6.040836051709557e-5
allele num: 66216
num of homozygotes: 0

African
type: Population
allele count: 370
allele frequency: 3.568672839506173e-2
allele num: 10368
num of homozygotes: 6

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8502
num of homozygotes: 0

Other
type: Population
allele count: 1
allele frequency: 1.106194690265487e-3
allele num: 904
num of homozygotes: 0

Latino
type: Population
allele count: 23
allele frequency: 1.997915218902015e-3
allele num: 11512
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16506
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 2.510973e6

QD
type: SiteQuality
SIO_000300: 1.563e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.04e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 5.1e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.07e-1

MQRankSum
type: SiteQuality
SIO_000300: 2.97e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 2.69e-2

MQ
type: SiteQuality
SIO_000300: 5.92e1

VQSLOD
type: SiteQuality
SIO_000300: 3.99e0

GenotypeQuality
all individuals: 190
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 77
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2368
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4519
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13961
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 636
bin: 2.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11548
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16506
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.516852228255923e-5
allele num: 65926
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10182
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 894
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8586
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.277e1

MQ
type: SiteQuality
SIO_000300: 5.968e1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.68e0

FS
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.28e0

DP
type: SiteQuality
SIO_000300: 2.27638e6

MQRankSum
type: SiteQuality
SIO_000300: 9.62e-1

VQSLOD
type: SiteQuality
SIO_000300: 8.03e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -5.05e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.1e-3

GenotypeQuality
all individuals: 8829
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 631
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3288
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2369
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4518
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 32
bin: 5.75e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10182
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16506
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.165229550221394e-4
allele num: 8582
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65936
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11546
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 896
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.16e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.938e0

FS
type: SiteQuality
SIO_000300: 8.829000000000001e0

VQSLOD
type: SiteQuality
SIO_000300: -2.411e0

BaseQRankSum
type: SiteQuality
SIO_000300: 3.82e0

DP
type: SiteQuality
SIO_000300: 2.278406e6

MQ
type: SiteQuality
SIO_000300: 5.909e1

MQRankSum
type: SiteQuality
SIO_000300: -2.78e-1

QD
type: SiteQuality
SIO_000300: 1.874e1

GenotypeQuality
all individuals: 27
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1532
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13956
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 3287
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8827
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 197
bin: 2.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16506
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.516346212167162e-5
allele num: 65948
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10192
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 896
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11544
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8580
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: -9.0e-2

MQ
type: SiteQuality
SIO_000300: 5.954e1

FS
type: SiteQuality
SIO_000300: 5.505e0

ClippingRankSum
type: SiteQuality
SIO_000300: -3.02e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.05e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 2.279006e6

VQSLOD
type: SiteQuality
SIO_000300: -1.799e0

QD
type: SiteQuality
SIO_000300: 2.158e1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.878e0

GenotypeQuality
all individuals: 245
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 29
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2368
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4515
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 8830
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 632
bin: 2.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8584
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.798157946306095e-5
allele num: 10206
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65956
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11548
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 896
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16506
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -4.51e-1

DP
type: SiteQuality
SIO_000300: 2.279907e6

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.2e-3

FS
type: SiteQuality
SIO_000300: 4.171e0

QD
type: SiteQuality
SIO_000300: 1.439e1

VQSLOD
type: SiteQuality
SIO_000300: 9.409999999999999e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.3e-2

MQRankSum
type: SiteQuality
SIO_000300: 3.15e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

BaseQRankSum
type: SiteQuality
SIO_000300: -4.349e0

GenotypeQuality
all individuals: 234
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2368
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8830
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3284
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 20
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 21120
bin: 6.25e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65956
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8584
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11548
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

South Asian
type: Population
allele count: 2
allele frequency: 1.211680600993578e-4
allele num: 16506
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10206
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 896
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 3.15e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -4.349e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

VQSLOD
type: SiteQuality
SIO_000300: 9.409999999999999e-1

FS
type: SiteQuality
SIO_000300: 4.171e0

DP
type: SiteQuality
SIO_000300: 2.279907e6

ClippingRankSum
type: SiteQuality
SIO_000300: -4.51e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.2e-3

QD
type: SiteQuality
SIO_000300: 1.439e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.3e-2

GenotypeQuality
all individuals: 69
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 231
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 61
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 13950
bin: 9.75e1
variant carriers: 17

GenotypeQuality
all individuals: 1528
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 21141
bin: 6.25e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10212
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8582
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16506
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

Latino
type: Population
allele count: 7
allele frequency: 6.061655697956356e-4
allele num: 11548
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 896
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 10
allele frequency: 1.516116316443798e-4
allele num: 65958
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.963e1

MQRankSum
type: SiteQuality
SIO_000300: 5.3e-2

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

QD
type: SiteQuality
SIO_000300: 1.556e1

DP
type: SiteQuality
SIO_000300: 2.280991e6

VQSLOD
type: SiteQuality
SIO_000300: 4.19e0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.95e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.074e0

FS
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.399999999999999e-1

GenotypeQuality
all individuals: 173
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 65
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 195
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3286
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 13937
bin: 9.75e1
variant carriers: 16

GenotypeQuality
all individuals: 57
bin: 5.25e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10222
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 896
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8588
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 4
allele frequency: 6.063913649869626e-5
allele num: 65964
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11548
num of homozygotes: 0

South Asian
type: Population
allele count: 12
allele frequency: 7.270083605961468e-4
allele num: 16506
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 1.08e0

VQSLOD
type: SiteQuality
SIO_000300: 2.81e0

MQ
type: SiteQuality
SIO_000300: 5.942e1

FS
type: SiteQuality
SIO_000300: 0.0e0

MQRankSum
type: SiteQuality
SIO_000300: -7.8e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.52e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 9.1e-2

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.999999999999999e-4

QD
type: SiteQuality
SIO_000300: 1.296e1

DP
type: SiteQuality
SIO_000300: 2.281737e6

GenotypeQuality
all individuals: 621
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3287
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4518
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 21321
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 13927
bin: 9.75e1
variant carriers: 2

GenotypeQuality
all individuals: 3405
bin: 8.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 1
allele frequency: 1.513317191283293e-4
allele num: 6608
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8590
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16502
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 894
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11546
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10224
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.515794579518584e-5
allele num: 65972
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 5.235e0

MQRankSum
type: SiteQuality
SIO_000300: 7.099999999999999e-2

BaseQRankSum
type: SiteQuality
SIO_000300: 5.86e-1

QD
type: SiteQuality
SIO_000300: 1.595e1

DP
type: SiteQuality
SIO_000300: 2.280978e6

ClippingRankSum
type: SiteQuality
SIO_000300: -7.64e-1

VQSLOD
type: SiteQuality
SIO_000300: 5.19e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.0e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.04e0

MQ
type: SiteQuality
SIO_000300: 5.955e1

GenotypeQuality
all individuals: 13926
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 2369
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4521
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 15
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1530
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 41
bin: 4.75e1
variant carriers: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.05913717886573e-5
allele num: 16504
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11548
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10240
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8590
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66008
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 896
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -4.0e-4

ClippingRankSum
type: SiteQuality
SIO_000300: -1.054e0

VQSLOD
type: SiteQuality
SIO_000300: 1.18e0

BaseQRankSum
type: SiteQuality
SIO_000300: -3.26e-1

FS
type: SiteQuality
SIO_000300: 8.206e0

MQRankSum
type: SiteQuality
SIO_000300: 8.169999999999999e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.42e0

QD
type: SiteQuality
SIO_000300: 1.55e1

DP
type: SiteQuality
SIO_000300: 2.283151e6

MQ
type: SiteQuality
SIO_000300: 5.962e1

GenotypeQuality
all individuals: 26
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 583
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 76
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4521
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2370
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 26
bin: 4.25e1
variant carriers: 0

South Asian
type: Population
allele count: 41
allele frequency: 2.484246243334949e-3
allele num: 16504
num of homozygotes: 1

African
type: Population
allele count: 1
allele frequency: 9.759906304899473e-5
allele num: 10246
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8590
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66026
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11548
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 894
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 0.0e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.52e-2

DP
type: SiteQuality
SIO_000300: 2.286962e6

ClippingRankSum
type: SiteQuality
SIO_000300: -4.27e-1

MQRankSum
type: SiteQuality
SIO_000300: 1.54e-1

QD
type: SiteQuality
SIO_000300: 1.902e1

BaseQRankSum
type: SiteQuality
SIO_000300: 2.8e-1

VQSLOD
type: SiteQuality
SIO_000300: 5.5e0

MQ
type: SiteQuality
SIO_000300: 6.017e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.7e-2

GenotypeQuality
all individuals: 2369
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8879
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 47
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 1528
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 21720
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 13887
bin: 9.75e1
variant carriers: 1

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8590
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 894
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10246
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.088650754992694e-5
allele num: 16424
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11548
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66032
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: -5.37e-1

MQ
type: SiteQuality
SIO_000300: 5.963e1

MQRankSum
type: SiteQuality
SIO_000300: -1.62e0

BaseQRankSum
type: SiteQuality
SIO_000300: 4.98e0

VQSLOD
type: SiteQuality
SIO_000300: -2.601e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -4.0e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.25e-1

QD
type: SiteQuality
SIO_000300: 1.464e1

DP
type: SiteQuality
SIO_000300: 2.281285e6

GenotypeQuality
all individuals: 8885
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 574
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 116
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 115
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 21520
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3406
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 78
bin: 3.75e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10246
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.514463122822959e-5
allele num: 66030
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8590
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16506
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11548
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 896
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.866e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.0e-4

DP
type: SiteQuality
SIO_000300: 2.283284e6

BaseQRankSum
type: SiteQuality
SIO_000300: -5.610000000000001e-1

MQRankSum
type: SiteQuality
SIO_000300: 2.03e0

VQSLOD
type: SiteQuality
SIO_000300: -1.997e0

FS
type: SiteQuality
SIO_000300: 3.488e0

ClippingRankSum
type: SiteQuality
SIO_000300: 7.3e-2

QD
type: SiteQuality
SIO_000300: 9.24e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.66e-1

GenotypeQuality
all individuals: 13900
bin: 9.75e1
variant carriers: 4

GenotypeQuality
all individuals: 84
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 73
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 566
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1528
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2367
bin: 9.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 896
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11548
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.028284174186906e-5
allele num: 66044
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16506
num of homozygotes: 0

African
type: Population
allele count: 2
allele frequency: 1.951981260979895e-4
allele num: 10246
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8590
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 8.87e-1

VQSLOD
type: SiteQuality
SIO_000300: 2.48e0

ClippingRankSum
type: SiteQuality
SIO_000300: -4.2e-1

DP
type: SiteQuality
SIO_000300: 2.283545e6

MQ
type: SiteQuality
SIO_000300: 5.734e1

QD
type: SiteQuality
SIO_000300: 1.401e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.0e-4

FS
type: SiteQuality
SIO_000300: 3.294e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.38e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -9.19e-1

GenotypeQuality
all individuals: 1526
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13896
bin: 9.75e1
variant carriers: 2

GenotypeQuality
all individuals: 27
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 25
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3407
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8890
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 59
bin: 5.25e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 894
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.027275754548482e-5
allele num: 66066
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10252
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8590
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11546
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16506
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.0e-4

DP
type: SiteQuality
SIO_000300: 2.283767e6

VQSLOD
type: SiteQuality
SIO_000300: 8.78e-1

QD
type: SiteQuality
SIO_000300: 1.12e1

ClippingRankSum
type: SiteQuality
SIO_000300: -5.0e-3

FS
type: SiteQuality
SIO_000300: 0.0e0

MQRankSum
type: SiteQuality
SIO_000300: 8.86e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -5.251e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.06e0

MQ
type: SiteQuality
SIO_000300: 5.977e1

GenotypeQuality
all individuals: 69
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3407
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 108
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13896
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 9
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 17
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 59
bin: 5.25e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16506
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.513821187441339e-5
allele num: 66058
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10254
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11546
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8592
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 894
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.932e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.0e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.11e-1

DP
type: SiteQuality
SIO_000300: 2.28373e6

BaseQRankSum
type: SiteQuality
SIO_000300: -2.762e0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.01e0

MQRankSum
type: SiteQuality
SIO_000300: -6.98e-1

QD
type: SiteQuality
SIO_000300: 1.1e1

FS
type: SiteQuality
SIO_000300: 0.0e0

VQSLOD
type: SiteQuality
SIO_000300: 4.41e-1

GenotypeQuality
all individuals: 581
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 14
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 13897
bin: 9.75e1
variant carriers: 2

GenotypeQuality
all individuals: 16
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3406
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2367
bin: 9.25e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.513821187441339e-5
allele num: 66058
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11546
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.163873370577281e-4
allele num: 8592
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 896
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10254
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16508
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.904e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.0e-4

ClippingRankSum
type: SiteQuality
SIO_000300: -2.13e-1

QD
type: SiteQuality
SIO_000300: 1.21e1

VQSLOD
type: SiteQuality
SIO_000300: 9.58e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

MQRankSum
type: SiteQuality
SIO_000300: -3.06e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.66e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.26e0

DP
type: SiteQuality
SIO_000300: 2.2839e6

GenotypeQuality
all individuals: 67
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 26
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8881
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4522
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3290
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1526
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 51
bin: 5.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66056
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11546
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8590
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.05766900896535e-5
allele num: 16508
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.75609756097561e-5
allele num: 10250
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 894
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 9.320000000000001e-1

MQ
type: SiteQuality
SIO_000300: 5.929e1

FS
type: SiteQuality
SIO_000300: 5.41e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -3.38e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.45e-1

DP
type: SiteQuality
SIO_000300: 2.283767e6

InbreedingCoeff
type: SiteQuality
SIO_000300: 7.0e-4

VQSLOD
type: SiteQuality
SIO_000300: 7.74e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.39e0

QD
type: SiteQuality
SIO_000300: 1.321e1

GenotypeQuality
all individuals: 18
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 21715
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1526
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13896
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 2368
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4522
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 8881
bin: 6.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66056
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11546
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 894
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16508
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8590
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.75609756097561e-5
allele num: 10250
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 5.41e-1

VQSLOD
type: SiteQuality
SIO_000300: 7.74e-1

MQRankSum
type: SiteQuality
SIO_000300: 9.320000000000001e-1

DP
type: SiteQuality
SIO_000300: 2.283767e6

MQ
type: SiteQuality
SIO_000300: 5.929e1

QD
type: SiteQuality
SIO_000300: 1.321e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 7.0e-4

ClippingRankSum
type: SiteQuality
SIO_000300: -3.38e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.39e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.45e-1

GenotypeQuality
all individuals: 45
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3284
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8867
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 27
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4521
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 125
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13892
bin: 9.75e1
variant carriers: 1

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11544
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65948
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.05913717886573e-5
allele num: 16504
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8576
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10236
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 892
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.1e-2

MQ
type: SiteQuality
SIO_000300: 5.859e1

MQRankSum
type: SiteQuality
SIO_000300: 5.06e-1

QD
type: SiteQuality
SIO_000300: 7.88e0

FS
type: SiteQuality
SIO_000300: 1.2328e1

ClippingRankSum
type: SiteQuality
SIO_000300: -4.62e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.0e-3

VQSLOD
type: SiteQuality
SIO_000300: -1.846e0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.128e0

DP
type: SiteQuality
SIO_000300: 2.281491e6

GenotypeQuality
all individuals: 4517
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3402
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 124
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 27
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 70
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 13891
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 87
bin: 4.75e1
variant carriers: 0

Latino
type: Population
allele count: 1
allele frequency: 8.662508662508663e-5
allele num: 11544
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10236
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16502
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8574
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65932
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.95e1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.429e0

MQRankSum
type: SiteQuality
SIO_000300: 1.06e0

FS
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
SIO_000300: 6.0e-2

VQSLOD
type: SiteQuality
SIO_000300: 2.26e-1

DP
type: SiteQuality
SIO_000300: 2.280973e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.89e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 7.0e-4

QD
type: SiteQuality
SIO_000300: 1.104e1

GenotypeQuality
all individuals: 138
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 62
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13890
bin: 9.75e1
variant carriers: 4

GenotypeQuality
all individuals: 1527
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3402
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8852
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 122
bin: 3.75e1
variant carriers: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.166861143523921e-4
allele num: 8570
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16502
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10232
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11544
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 3
allele frequency: 4.552490212146044e-5
allele num: 65898
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: -9.6e-1

VQSLOD
type: SiteQuality
SIO_000300: 1.61e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.05e0

BaseQRankSum
type: SiteQuality
SIO_000300: -3.2e-1

DP
type: SiteQuality
SIO_000300: 2.280813e6

InbreedingCoeff
type: SiteQuality
SIO_000300: 9.0e-4

MQRankSum
type: SiteQuality
SIO_000300: -6.97e-1

QD
type: SiteQuality
SIO_000300: 1.405e1

MQ
type: SiteQuality
SIO_000300: 5.967e1

GenotypeQuality
all individuals: 135
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4517
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 66
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 1527
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2368
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3403
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 90
bin: 4.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8570
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10238
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11544
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.517312536036173e-5
allele num: 65906
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16502
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -4.418e-1

MQRankSum
type: SiteQuality
SIO_000300: 2.03e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 7.0e-4

QD
type: SiteQuality
SIO_000300: 9.380000000000001e0

FS
type: SiteQuality
SIO_000300: 4.487e0

BaseQRankSum
type: SiteQuality
SIO_000300: -4.026e0

ClippingRankSum
type: SiteQuality
SIO_000300: -2.615e0

DP
type: SiteQuality
SIO_000300: 2.280293e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.47e0

MQ
type: SiteQuality
SIO_000300: 5.942e1

GenotypeQuality
all individuals: 746
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 13889
bin: 9.75e1
variant carriers: 17

GenotypeQuality
all individuals: 142
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4513
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3280
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 21383
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 56
bin: 4.25e1
variant carriers: 0

African
type: Population
allele count: 13
allele frequency: 1.270275552081298e-3
allele num: 10234
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.036007043536341e-5
allele num: 65876
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8568
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16500
num of homozygotes: 0

Latino
type: Population
allele count: 2
allele frequency: 1.732501732501733e-4
allele num: 11544
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6606
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 2.281577e6

FS
type: SiteQuality
SIO_000300: 5.3e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.0e-4

VQSLOD
type: SiteQuality
SIO_000300: 1.7e0

ClippingRankSum
type: SiteQuality
SIO_000300: -3.37e-1

QD
type: SiteQuality
SIO_000300: 1.027e1

MQRankSum
type: SiteQuality
SIO_000300: 5.7e-2

BaseQRankSum
type: SiteQuality
SIO_000300: 4.42e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.08e-1

MQ
type: SiteQuality
SIO_000300: 5.941e1

GenotypeQuality
all individuals: 8
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 1530
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 149
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3401
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2367
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 77
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13873
bin: 9.75e1
variant carriers: 1

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8564
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10224
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11542
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16500
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.51851064475962e-5
allele num: 65854
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.145e1

FS
type: SiteQuality
SIO_000300: 1.0096e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.999999999999999e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.2e-1

MQRankSum
type: SiteQuality
SIO_000300: -1.476e0

VQSLOD
type: SiteQuality
SIO_000300: -1.496e0

MQ
type: SiteQuality
SIO_000300: 5.945e1

ClippingRankSum
type: SiteQuality
SIO_000300: -6.72e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 8.9e-2

DP
type: SiteQuality
SIO_000300: 2.278253e6

GenotypeQuality
all individuals: 8823
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1529
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 44
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3400
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4511
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2367
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 75
bin: 5.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8564
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10218
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.06134076857801e-5
allele num: 16498
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 4
allele frequency: 6.0779189205616e-5
allele num: 65812
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11542
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 1.126e0

MQRankSum
type: SiteQuality
SIO_000300: 1.3e0

BaseQRankSum
type: SiteQuality
SIO_000300: 4.75e-1

QD
type: SiteQuality
SIO_000300: 9.720000000000001e0

VQSLOD
type: SiteQuality
SIO_000300: 3.56e-1

MQ
type: SiteQuality
SIO_000300: 5.953e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.97e-1

DP
type: SiteQuality
SIO_000300: 2.278148e6

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.0e-4

ClippingRankSum
type: SiteQuality
SIO_000300: -9.340000000000001e-1

GenotypeQuality
all individuals: 790
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 154
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 72
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 4514
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13867
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 8820
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 72
bin: 4.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6606
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16498
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10220
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11542
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65810
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.16767865483419e-4
allele num: 8564
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.057e1

FS
type: SiteQuality
SIO_000300: 2.526e0

BaseQRankSum
type: SiteQuality
SIO_000300: 1.26e0

VQSLOD
type: SiteQuality
SIO_000300: 2.09e-1

DP
type: SiteQuality
SIO_000300: 2.27727e6

MQ
type: SiteQuality
SIO_000300: 5.963e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.0e-4

MQRankSum
type: SiteQuality
SIO_000300: -7.9e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -9.19e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.47e0

GenotypeQuality
all individuals: 38
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1529
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 17
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 74
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 108
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3398
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 80
bin: 5.25e1
variant carriers: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.16795141322121e-4
allele num: 8562
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.06134076857801e-5
allele num: 16498
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.519756838905775e-5
allele num: 65800
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10218
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11542
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 1.38e0

FS
type: SiteQuality
SIO_000300: 0.0e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.999999999999999e-4

MQ
type: SiteQuality
SIO_000300: 5.954e1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.772e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.62e-1

MQRankSum
type: SiteQuality
SIO_000300: 6.02e-1

QD
type: SiteQuality
SIO_000300: 9.279999999999999e0

DP
type: SiteQuality
SIO_000300: 2.277146e6

ClippingRankSum
type: SiteQuality
SIO_000300: -3.1e-2

GenotypeQuality
all individuals: 3275
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 27
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1529
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 84
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 13865
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 3398
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2367
bin: 9.25e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.519710647092794e-5
allele num: 65802
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10220
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16496
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8560
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11542
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 7.77e-1

MQRankSum
type: SiteQuality
SIO_000300: -1.562e0

FS
type: SiteQuality
SIO_000300: 2.247e0

VQSLOD
type: SiteQuality
SIO_000300: -9.133e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.999999999999999e-4

ClippingRankSum
type: SiteQuality
SIO_000300: -5.36e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.22e0

DP
type: SiteQuality
SIO_000300: 2.276842e6

QD
type: SiteQuality
SIO_000300: 9.140000000000001e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
all individuals: 140
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 799
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4507
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1529
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3399
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2367
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 33
bin: 5.75e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10216
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8564
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65796
num of homozygotes: 0

South Asian
type: Population
allele count: 12
allele frequency: 7.273608922293612e-4
allele num: 16498
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11542
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 888
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 1.71e0

FS
type: SiteQuality
SIO_000300: 0.0e0

MQRankSum
type: SiteQuality
SIO_000300: 3.3e-2

VQSLOD
type: SiteQuality
SIO_000300: 9.91e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.29e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.093e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.0e-4

MQ
type: SiteQuality
SIO_000300: 5.941e1

DP
type: SiteQuality
SIO_000300: 2.277667e6

QD
type: SiteQuality
SIO_000300: 1.171e1

GenotypeQuality
all individuals: 129
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 13861
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 45
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4506
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 58
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 21444
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3397
bin: 8.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8556
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10208
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16498
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65756
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.668515950069348e-5
allele num: 11536
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 2.275892e6

InbreedingCoeff
type: SiteQuality
SIO_000300: 8.0e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.74e0

MQRankSum
type: SiteQuality
SIO_000300: 2.46e-1

VQSLOD
type: SiteQuality
SIO_000300: 6.840000000000001e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 7.07e-1

FS
type: SiteQuality
SIO_000300: 5.53e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.5e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 1.231e1

GenotypeQuality
all individuals: 58
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 32
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1529
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4506
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 45
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3397
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 29
bin: 5.75e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10208
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11536
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16498
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8556
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.52077376969402e-5
allele num: 65756
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 6.840000000000001e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 7.07e-1

FS
type: SiteQuality
SIO_000300: 5.53e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 1.231e1

DP
type: SiteQuality
SIO_000300: 2.275892e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.74e0

MQRankSum
type: SiteQuality
SIO_000300: 2.46e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.5e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 8.0e-4

GenotypeQuality
all individuals: 3396
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 74
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 38
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 12
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 35
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 8819
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4503
bin: 7.75e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11534
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16498
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10214
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.043676761527926e-5
allele num: 65710
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8552
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.34e0

QD
type: SiteQuality
SIO_000300: 1.123e1

MQ
type: SiteQuality
SIO_000300: 5.96e1

DP
type: SiteQuality
SIO_000300: 2.275392e6

ClippingRankSum
type: SiteQuality
SIO_000300: 6.81e-1

VQSLOD
type: SiteQuality
SIO_000300: 8.19e-1

FS
type: SiteQuality
SIO_000300: 2.849e0

MQRankSum
type: SiteQuality
SIO_000300: 2.65e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 5.34e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.0e-4

GenotypeQuality
all individuals: 34
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1529
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 67
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3396
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 21342
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 43
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13858
bin: 9.75e1
variant carriers: 12

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

Latino
type: Population
allele count: 6
allele frequency: 5.202011444425178e-4
allele num: 11534
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8546
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10204
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 6
allele frequency: 9.134644662322636e-5
allele num: 65684
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16498
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 1.83e0

DP
type: SiteQuality
SIO_000300: 2.275952e6

ClippingRankSum
type: SiteQuality
SIO_000300: -5.12e-1

QD
type: SiteQuality
SIO_000300: 1.389e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 2.0e-4

BaseQRankSum
type: SiteQuality
SIO_000300: -3.62e-1

MQRankSum
type: SiteQuality
SIO_000300: 8.27e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.62e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

MQ
type: SiteQuality
SIO_000300: 5.938e1

GenotypeQuality
all individuals: 8813
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 93
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 14
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2367
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 31
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3397
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1530
bin: 8.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.522672594938636e-5
allele num: 65674
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.803921568627451e-5
allele num: 10200
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11534
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8546
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16494
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 2.274139e6

BaseQRankSum
type: SiteQuality
SIO_000300: 4.01e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.0e-4

VQSLOD
type: SiteQuality
SIO_000300: 3.2e0

MQRankSum
type: SiteQuality
SIO_000300: 6.68e-1

QD
type: SiteQuality
SIO_000300: 1.403e1

FS
type: SiteQuality
SIO_000300: 4.65e-1

MQ
type: SiteQuality
SIO_000300: 6.028e1

ReadPosRankSum
type: SiteQuality
SIO_000300: -4.03e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.91e-1

GenotypeQuality
all individuals: 3397
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2367
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 40
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 10
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 68
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1530
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13845
bin: 9.75e1
variant carriers: 2

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

South Asian
type: Population
allele count: 2
allele frequency: 1.21256214380987e-4
allele num: 16494
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65644
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10182
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8542
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11532
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 2.27375e6

VQSLOD
type: SiteQuality
SIO_000300: -2.936e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 2.0e-4

BaseQRankSum
type: SiteQuality
SIO_000300: 2.99e0

FS
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 2.655e1

MQ
type: SiteQuality
SIO_000300: 5.916e1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.284e0

MQRankSum
type: SiteQuality
SIO_000300: -7.24e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.54e0

GenotypeQuality
all individuals: 136
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 13844
bin: 9.75e1
variant carriers: 3

GenotypeQuality
all individuals: 2366
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3397
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 32
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 44
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 37
bin: 4.25e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16494
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 888
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11532
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

African
type: Population
allele count: 2
allele frequency: 1.965022597759874e-4
allele num: 10178
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8542
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.523507724184162e-5
allele num: 65638
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 1.426e1

DP
type: SiteQuality
SIO_000300: 2.273571e6

ClippingRankSum
type: SiteQuality
SIO_000300: -2.75e-1

MQ
type: SiteQuality
SIO_000300: 5.944e1

VQSLOD
type: SiteQuality
SIO_000300: 4.04e0

MQRankSum
type: SiteQuality
SIO_000300: 3.24e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.999999999999999e-4

BaseQRankSum
type: SiteQuality
SIO_000300: -3.264e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.09e0

GenotypeQuality
all individuals: 8780
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 44
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 60
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4496
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13842
bin: 9.75e1
variant carriers: 3

GenotypeQuality
all individuals: 21264
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2366
bin: 9.25e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16492
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8524
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 3
allele frequency: 4.577916132576451e-5
allele num: 65532
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6606
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10164
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11520
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 6.014e1

BaseQRankSum
type: SiteQuality
SIO_000300: 6.0e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: -5.99e-1

FS
type: SiteQuality
SIO_000300: 2.301e0

QD
type: SiteQuality
SIO_000300: 1.597e1

MQRankSum
type: SiteQuality
SIO_000300: 4.02e-1

VQSLOD
type: SiteQuality
SIO_000300: 2.59e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.999999999999999e-4

DP
type: SiteQuality
SIO_000300: 2.271094e6

ClippingRankSum
type: SiteQuality
SIO_000300: -1.48e0

GenotypeQuality
all individuals: 179
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 54
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 13840
bin: 9.75e1
variant carriers: 3

GenotypeQuality
all individuals: 33
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 21208
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8769
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3395
bin: 8.25e1
variant carriers: 0

Latino
type: Population
allele count: 2
allele frequency: 1.736714136853074e-4
allele num: 11516
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10158
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8522
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6606
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.527090587013621e-5
allele num: 65484
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16492
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.925e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.999999999999999e-4

DP
type: SiteQuality
SIO_000300: 2.270056e6

VQSLOD
type: SiteQuality
SIO_000300: 3.68e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.01e0

QD
type: SiteQuality
SIO_000300: 1.278e1

MQRankSum
type: SiteQuality
SIO_000300: 5.78e-1

FS
type: SiteQuality
SIO_000300: 6.75e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -7.71e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.736e0

GenotypeQuality
all individuals: 24
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8767
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 65
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13837
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 3394
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 21165
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 15
bin: 5.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8514
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11514
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65446
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6606
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16488
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.854158454867954e-5
allele num: 10148
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.201e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.01e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.999999999999999e-4

VQSLOD
type: SiteQuality
SIO_000300: 1.76e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.898e0

MQ
type: SiteQuality
SIO_000300: 5.94e1

MQRankSum
type: SiteQuality
SIO_000300: 5.94e-1

DP
type: SiteQuality
SIO_000300: 2.268483e6

QD
type: SiteQuality
SIO_000300: 7.31e0

GenotypeQuality
all individuals: 11
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 2366
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3243
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3394
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 85
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13835
bin: 9.75e1
variant carriers: 4

GenotypeQuality
all individuals: 210
bin: 3.25e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16482
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 886
num of homozygotes: 0

East Asian
type: Population
allele count: 3
allele frequency: 3.532736693358455e-4
allele num: 8492
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6600
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10084
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11510
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.532191340054546e-5
allele num: 65266
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 1.22e0

ClippingRankSum
type: SiteQuality
SIO_000300: -3.92e-1

MQ
type: SiteQuality
SIO_000300: 5.982e1

BaseQRankSum
type: SiteQuality
SIO_000300: 4.62e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.43e0

QD
type: SiteQuality
SIO_000300: 1.36e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.999999999999999e-4

MQRankSum
type: SiteQuality
SIO_000300: 4.8e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 2.264429e6

GenotypeQuality
all individuals: 231
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4486
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 8732
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 40
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2366
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3242
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3395
bin: 8.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6600
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11510
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8492
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.532332209623046e-5
allele num: 65260
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 886
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10082
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16482
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.999999999999999e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.17e-1

VQSLOD
type: SiteQuality
SIO_000300: 7.69e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -5.705e0

MQ
type: SiteQuality
SIO_000300: 5.966e1

FS
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 1.112e1

MQRankSum
type: SiteQuality
SIO_000300: 1.02e0

ClippingRankSum
type: SiteQuality
SIO_000300: -8.22e-1

DP
type: SiteQuality
SIO_000300: 2.263624e6

GenotypeQuality
all individuals: 1529
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 107
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2364
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 111
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3395
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 20364
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 249
bin: 3.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8474
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.537704514700455e-5
allele num: 65032
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10024
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11500
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 882
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6594
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16472
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -6.142e-1

MQRankSum
type: SiteQuality
SIO_000300: 9.6e-1

FS
type: SiteQuality
SIO_000300: 9.098000000000001e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.14e0

ClippingRankSum
type: SiteQuality
SIO_000300: -4.93e-1

QD
type: SiteQuality
SIO_000300: 1.366e1

BaseQRankSum
type: SiteQuality
SIO_000300: 4.76e0

MQ
type: SiteQuality
SIO_000300: 5.962e1

DP
type: SiteQuality
SIO_000300: 2.257856e6

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.0e-4