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nstd39 (Schuster et al. 2010)

Organism:
Human
Study Type:
Control Set
Submitter:
Evan Eichler
Description:
Here we present the complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and a Bantu from southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, including 13,146 novel amino acid variants. See Variant Summary counts for nstd39 in dbVar Variant Summary.
Publication(s):
Schuster et al. 2010

Detailed Information: Download 187 Variant Regions, Download 187 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Remapped: GRCh37.p13 (hg19)
Submitted: NCBI35 (hg17)

Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.11Chr12727RemappedNC_000001.11
NC_000002.12Chr21414RemappedNC_000002.12
NC_000003.12Chr355RemappedNC_000003.12
NC_000004.12Chr444RemappedNC_000004.12
NC_000005.10Chr533RemappedNC_000005.10
NC_000006.12Chr655RemappedNC_000006.12
NC_000007.14Chr71717RemappedNC_000007.14
NC_000008.11Chr899RemappedNC_000008.11
NC_000009.12Chr966RemappedNC_000009.12
NC_000010.11Chr1088RemappedNC_000010.11
NC_000011.10Chr111010RemappedNC_000011.10
NC_000012.12Chr1222RemappedNC_000012.12
NC_000013.11Chr1322RemappedNC_000013.11
NC_000014.9Chr1444RemappedNC_000014.9
NC_000015.10Chr1566RemappedNC_000015.10
NC_000016.10Chr161818RemappedNC_000016.10
NC_000017.11Chr1755RemappedNC_000017.11
NC_000019.10Chr192727RemappedNC_000019.10
NC_000020.11Chr2066RemappedNC_000020.11
NC_000022.11Chr2288RemappedNC_000022.11
NT_187528.1Chr2|NT_187528.122RemappedNT_187528.1
NT_187539.1Chr3|NT_187539.111RemappedNT_187539.1
NT_167248.2Chr6|NT_167248.211RemappedNT_167248.2
NT_167245.2Chr6|NT_167245.211RemappedNT_167245.2
NT_113891.3Chr6|NT_113891.311RemappedNT_113891.3
NT_167244.2Chr6|NT_167244.211RemappedNT_167244.2
NW_018654714.1Chr7|NW_018654714.111RemappedNW_018654714.1
NW_018654715.1Chr7|NW_018654715.111RemappedNW_018654715.1
NW_018654716.1Chr8|NW_018654716.111RemappedNW_018654716.1
NW_018654717.1Chr8|NW_018654717.144RemappedNW_018654717.1
NT_187681.1Chr11|NT_187681.111RemappedNT_187681.1
NT_187656.1Chr11|NT_187656.111RemappedNT_187656.1
NW_015148966.1Chr11|NW_015148966.111RemappedNW_015148966.1
NT_187658.1Chr12|NT_187658.111RemappedNT_187658.1
NT_187588.1Chr12|NT_187588.111RemappedNT_187588.1
NW_018654722.1Chr14|NW_018654722.122RemappedNW_018654722.1
NT_187659.1Chr15|NT_187659.111RemappedNT_187659.1
NT_187660.1Chr15|NT_187660.111RemappedNT_187660.1
NT_187603.1Chr15|NT_187603.111RemappedNT_187603.1
NT_187604.1Chr15|NT_187604.111RemappedNT_187604.1
NW_011332701.1Chr15|NW_011332701.111RemappedNW_011332701.1
NW_018654723.1Chr16|NW_018654723.122RemappedNW_018654723.1
NT_187663.1Chr17|NT_187663.111RemappedNT_187663.1
NT_167251.2Chr17|NT_167251.211RemappedNT_167251.2
NW_009646206.1Chr19|NW_009646206.111RemappedNW_009646206.1
NT_187633.1Chr22|NT_187633.133RemappedNT_187633.1
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.10Chr12727RemappedNC_000001.10
NC_000002.11Chr21414RemappedNC_000002.11
NC_000003.11Chr355RemappedNC_000003.11
NC_000004.11Chr433RemappedNC_000004.11
NC_000005.9Chr533RemappedNC_000005.9
NC_000006.11Chr655RemappedNC_000006.11
NC_000007.13Chr71717RemappedNC_000007.13
NC_000008.10Chr899RemappedNC_000008.10
NC_000009.11Chr966RemappedNC_000009.11
NC_000010.10Chr1088RemappedNC_000010.10
NC_000011.9Chr111010RemappedNC_000011.9
NC_000012.11Chr1222RemappedNC_000012.11
NC_000013.10Chr1322RemappedNC_000013.10
NC_000014.8Chr1444RemappedNC_000014.8
NC_000015.9Chr1566RemappedNC_000015.9
NC_000016.9Chr161818RemappedNC_000016.9
NC_000017.10Chr1755RemappedNC_000017.10
NC_000019.9Chr192727RemappedNC_000019.9
NC_000020.10Chr2066RemappedNC_000020.10
NC_000022.10Chr2299RemappedNC_000022.10
NW_003571032.1Chr2|NW_003571032.111RemappedNW_003571032.1
NW_003571034.1Chr4|NW_003571034.111RemappedNW_003571034.1
NT_113891.2Chr6|NT_113891.211RemappedNT_113891.2
NT_167244.1Chr6|NT_167244.111RemappedNT_167244.1
NT_167245.1Chr6|NT_167245.111RemappedNT_167245.1
NT_167248.1Chr6|NT_167248.111RemappedNT_167248.1
NW_003871064.1Chr7|NW_003871064.133RemappedNW_003871064.1
NW_003315924.1Chr8|NW_003315924.111RemappedNW_003315924.1
NW_003871068.1Chr10|NW_003871068.122RemappedNW_003871068.1
NW_003871080.1Chr11|NW_003871080.111RemappedNW_003871080.1
NT_167251.1Chr17|NT_167251.111RemappedNT_167251.1
NW_004775434.1Chr19|NW_004775434.111RemappedNW_004775434.1
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.8Chr12727SubmittedNC_000001.8
NC_000002.9Chr21414SubmittedNC_000002.9
NC_000003.9Chr355SubmittedNC_000003.9
NC_000004.9Chr444SubmittedNC_000004.9
NC_000005.8Chr533SubmittedNC_000005.8
NC_000006.9Chr655SubmittedNC_000006.9
NC_000007.11Chr71717SubmittedNC_000007.11
NC_000008.9Chr899SubmittedNC_000008.9
NC_000009.9Chr966SubmittedNC_000009.9
NC_000010.8Chr1088SubmittedNC_000010.8
NC_000011.8Chr111010SubmittedNC_000011.8
NC_000012.9Chr1222SubmittedNC_000012.9
NC_000013.9Chr1322SubmittedNC_000013.9
NC_000014.7Chr1444SubmittedNC_000014.7
NC_000015.8Chr1566SubmittedNC_000015.8
NC_000016.8Chr161818SubmittedNC_000016.8
NC_000017.9Chr1755SubmittedNC_000017.9
NC_000019.8Chr192727SubmittedNC_000019.8
NC_000020.9Chr2066SubmittedNC_000020.9
NC_000022.8Chr2299SubmittedNC_000022.8

Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000001.8Chr12725200027252000
NC_000002.9Chr21413000114130001
NC_000003.9Chr3550000550000
NC_000004.9Chr4440000440000
NC_000005.8Chr5330000330000
NC_000006.9Chr6540001540001
NC_000007.11Chr71712110317121103
NC_000008.9Chr8980001980001
NC_000009.9Chr9660000660000
NC_000010.8Chr10860002860002
NC_000011.8Chr1110900011090001
NC_000012.9Chr12220000220000
NC_000013.9Chr13220000220000
NC_000014.7Chr14440000440000
NC_000015.8Chr15660000660000
NC_000016.8Chr161818000018180000
NC_000017.9Chr17540001540001
NC_000019.8Chr192726000127260001
NC_000020.9Chr20660000660000
NC_000022.8Chr22990000990000
Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000001.8Chr12725200027252000
NC_000002.9Chr21412000214120002
NC_000003.9Chr3540001540001
NC_000004.9Chr4440000440000
NC_000005.8Chr5330000330000
NC_000006.9Chr6531001531001
NC_000007.11Chr71710500217105002
NC_000008.9Chr8940005940005
NC_000009.9Chr9651000651000
NC_000010.8Chr10880000880000
NC_000011.8Chr1110810011081001
NC_000012.9Chr12200002200002
NC_000013.9Chr13220000220000
NC_000014.7Chr14420002420002
NC_000015.8Chr15630003630003
NC_000016.8Chr161816000218160002
NC_000017.9Chr17540001540001
NC_000019.8Chr192725100127251001
NC_000020.9Chr20660000660000
NC_000022.8Chr22970002970002

Samplesets

Number of Samplesets: 1

Size:
1
Organisms:
Homo sapiens
Sampleset Phenotype(s):
None reported
Sex:
Male
  • Download Samples as CSV file
  • Samples for sampleset 1
    Sample IDSubject ID SexEthnicitySubject Phenotype
    KB1KB1MaleSanNot reported

    Experimental Details

    Experiment IDTypeMethodAnalysisPlatformsDataNumber of Variant Calls
    1DiscoverySequencingRead depthIllumina Genome Analyzer and Roche/454 sequencer. For arrayCGH validation experiments we used NimblegenSRA, http://main.g2.bx.psu.edu/bushman187
    2ValidationOligo aCGHProbe signal intensity187

    Validations

    Experiment IDMethodAnalysisNumber of Variant Calls Validated
    2Oligo aCGHProbe signal intensity187
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