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nstd31 (Alkan et al. 2009)

Organism:
Human
Study Type:
Control Set
Submitter:
Evan Eichler
Description:
We present an algorithm (mrFAST) to comprehensively map next-generation sequence reads, which allows for the prediction of absolute copy-number variation of duplicated segments and genes. We examine three human genomes and experimentally validate genome-wide copy number differences. Our method provides a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based technology. See Variant Summary counts for nstd31 in dbVar Variant Summary.
Publication(s):
Alkan et al. 2009

Detailed Information: Download 226 Variant Regions, Download 607 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_000001.11Chr12773RemappedNC_000001.11
NC_000002.12Chr2617RemappedNC_000002.12
NC_000003.12Chr3412RemappedNC_000003.12
NC_000004.12Chr439RemappedNC_000004.12
NC_000005.10Chr51949RemappedNC_000005.10
NC_000006.12Chr6822RemappedNC_000006.12
NC_000007.14Chr72575RemappedNC_000007.14
NC_000008.11Chr82461RemappedNC_000008.11
NC_000009.12Chr9514RemappedNC_000009.12
NC_000010.11Chr10412RemappedNC_000010.11
NC_000011.10Chr11814RemappedNC_000011.10
NC_000012.12Chr1226RemappedNC_000012.12
NC_000013.11Chr1313RemappedNC_000013.11
NC_000014.9Chr14719RemappedNC_000014.9
NC_000015.10Chr151937RemappedNC_000015.10
NC_000016.10Chr161339RemappedNC_000016.10
NC_000017.11Chr172467RemappedNC_000017.11
NC_000018.10Chr1813RemappedNC_000018.10
NC_000019.10Chr191030RemappedNC_000019.10
NC_000021.9Chr2113RemappedNC_000021.9
NC_000022.11Chr22616RemappedNC_000022.11
NT_187528.1Chr2|NT_187528.113RemappedNT_187528.1
NT_187678.1Chr3|NT_187678.113RemappedNT_187678.1
NT_187688.1Chr3|NT_187688.113RemappedNT_187688.1
NT_187689.1Chr3|NT_187689.113RemappedNT_187689.1
NT_187690.1Chr3|NT_187690.113RemappedNT_187690.1
NT_187691.1Chr3|NT_187691.113RemappedNT_187691.1
NT_187532.1Chr3|NT_187532.113RemappedNT_187532.1
NT_187539.1Chr3|NT_187539.113RemappedNT_187539.1
NT_187649.1Chr3|NT_187649.113RemappedNT_187649.1
NT_167250.2Chr4|NT_167250.213RemappedNT_167250.2
NT_187651.1Chr5|NT_187651.1920RemappedNT_187651.1
NW_003315917.2Chr5|NW_003315917.2715RemappedNW_003315917.2
NT_167247.2Chr6|NT_167247.2515RemappedNT_167247.2
NT_167248.2Chr6|NT_167248.2515RemappedNT_167248.2
NT_167249.2Chr6|NT_167249.2515RemappedNT_167249.2
NT_167245.2Chr6|NT_167245.2616RemappedNT_167245.2
NT_187561.1Chr7|NT_187561.113RemappedNT_187561.1
NW_018654715.1Chr7|NW_018654715.139RemappedNW_018654715.1
NT_187570.1Chr8|NT_187570.1613RemappedNT_187570.1
NW_018654717.1Chr8|NW_018654717.11333RemappedNW_018654717.1
NW_003571050.1Chr12|NW_003571050.113RemappedNW_003571050.1
NW_011332699.1Chr13|NW_011332699.113RemappedNW_011332699.1
NT_187603.1Chr15|NT_187603.133RemappedNT_187603.1
NT_187607.1Chr16|NT_187607.126RemappedNT_187607.1
NW_017852933.1Chr16|NW_017852933.113RemappedNW_017852933.1
NT_187661.1Chr17|NT_187661.1617RemappedNT_187661.1
NT_187663.1Chr17|NT_187663.136RemappedNT_187663.1
NT_167251.2Chr17|NT_167251.225RemappedNT_167251.2
NT_187614.1Chr17|NT_187614.1412RemappedNT_187614.1
NW_003871092.1Chr17|NW_003871092.113RemappedNW_003871092.1
NT_187693.1Chr19|NT_187693.113RemappedNT_187693.1
NW_009646206.1Chr19|NW_009646206.113RemappedNW_009646206.1
NT_187633.1Chr22|NT_187633.124RemappedNT_187633.1
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.10Chr12773RemappedNC_000001.10
NC_000002.11Chr2617RemappedNC_000002.11
NC_000003.11Chr3412RemappedNC_000003.11
NC_000004.11Chr426RemappedNC_000004.11
NC_000005.9Chr51949RemappedNC_000005.9
NC_000006.11Chr6822RemappedNC_000006.11
NC_000007.13Chr72575RemappedNC_000007.13
NC_000008.10Chr82461RemappedNC_000008.10
NC_000009.11Chr9514RemappedNC_000009.11
NC_000010.10Chr10412RemappedNC_000010.10
NC_000011.9Chr11814RemappedNC_000011.9
NC_000012.11Chr1226RemappedNC_000012.11
NC_000013.10Chr1313RemappedNC_000013.10
NC_000014.8Chr14719RemappedNC_000014.8
NC_000015.9Chr151937RemappedNC_000015.9
NC_000016.9Chr161339RemappedNC_000016.9
NC_000017.10Chr172672RemappedNC_000017.10
NC_000018.9Chr1813RemappedNC_000018.9
NC_000019.9Chr191133RemappedNC_000019.9
NC_000021.8Chr2113RemappedNC_000021.8
NC_000022.10Chr22822RemappedNC_000022.10
NT_167250.1Chr4|NT_167250.113RemappedNT_167250.1
NW_003571034.1Chr4|NW_003571034.113RemappedNW_003571034.1
NW_003315917.2Chr5|NW_003315917.2715RemappedNW_003315917.2
NW_004775428.1Chr5|NW_004775428.126RemappedNW_004775428.1
NT_113891.2Chr6|NT_113891.213RemappedNT_113891.2
NT_167245.1Chr6|NT_167245.1616RemappedNT_167245.1
NT_167247.1Chr6|NT_167247.1515RemappedNT_167247.1
NT_167248.1Chr6|NT_167248.1515RemappedNT_167248.1
NT_167249.1Chr6|NT_167249.1515RemappedNT_167249.1
NW_003871064.1Chr7|NW_003871064.113RemappedNW_003871064.1
NW_003871067.1Chr9|NW_003871067.113RemappedNW_003871067.1
NW_004504302.1Chr10|NW_004504302.113RemappedNW_004504302.1
NW_003571050.1Chr12|NW_003571050.113RemappedNW_003571050.1
NT_167251.1Chr17|NT_167251.113RemappedNT_167251.1
NW_003315949.1Chr17|NW_003315949.126RemappedNW_003315949.1
NW_003871086.1Chr17|NW_003871086.111RemappedNW_003871086.1
NW_003871088.1Chr17|NW_003871088.113RemappedNW_003871088.1
NW_003871092.1Chr17|NW_003871092.113RemappedNW_003871092.1
NW_004166865.1Chr19|NW_004166865.113RemappedNW_004166865.1
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.8Chr12773SubmittedNC_000001.8
NC_000002.9Chr2617SubmittedNC_000002.9
NC_000003.9Chr3412SubmittedNC_000003.9
NC_000004.9Chr4412SubmittedNC_000004.9
NC_000005.8Chr51949SubmittedNC_000005.8
NC_000006.9Chr6822SubmittedNC_000006.9
NC_000007.11Chr72575SubmittedNC_000007.11
NC_000008.9Chr82461SubmittedNC_000008.9
NC_000009.9Chr9514SubmittedNC_000009.9
NC_000010.8Chr10412SubmittedNC_000010.8
NC_000011.8Chr11814SubmittedNC_000011.8
NC_000012.9Chr1226SubmittedNC_000012.9
NC_000013.9Chr1313SubmittedNC_000013.9
NC_000014.7Chr14719SubmittedNC_000014.7
NC_000015.8Chr151937SubmittedNC_000015.8
NC_000016.8Chr161339SubmittedNC_000016.8
NC_000017.9Chr172878SubmittedNC_000017.9
NC_000018.8Chr1813SubmittedNC_000018.8
NC_000019.8Chr191236SubmittedNC_000019.8
NC_000021.7Chr2113SubmittedNC_000021.7
NC_000022.8Chr22822SubmittedNC_000022.8

Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000001.8Chr12727000073730000
NC_000002.9Chr266000017170000
NC_000003.9Chr344000012120000
NC_000004.9Chr44310001293000
NC_000005.8Chr519100009492800021
NC_000006.9Chr682000622600016
NC_000007.11Chr725185101755415303
NC_000008.9Chr82424000061610000
NC_000009.9Chr954000114110003
NC_000010.8Chr104300011290003
NC_000011.8Chr1188000014140000
NC_000012.9Chr12210001630003
NC_000013.9Chr13110000330000
NC_000014.7Chr1474300019109000
NC_000015.8Chr151915400037298000
NC_000016.8Chr161313000039390000
NC_000017.9Chr172814550478401315010
NC_000018.8Chr18110000330000
NC_000019.8Chr191212000036360000
NC_000021.7Chr21110000330000
NC_000022.8Chr2288000022220000
Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000001.8Chr12726100073703000
NC_000002.9Chr265000117140003
NC_000003.9Chr34200021260006
NC_000004.9Chr44310001293000
NC_000005.8Chr519100009492900020
NC_000006.9Chr682000622600016
NC_000007.11Chr7251470047542210012
NC_000008.9Chr824500019611500046
NC_000009.9Chr955000014140000
NC_000010.8Chr104202001260600
NC_000011.8Chr1188000014140000
NC_000012.9Chr12210001630003
NC_000013.9Chr13110000330000
NC_000014.7Chr1474030019100900
NC_000015.8Chr151915100337313003
NC_000016.8Chr16139010339270309
NC_000017.9Chr17281251197834143324
NC_000018.8Chr18110000330000
NC_000019.8Chr191211010036330300
NC_000021.7Chr21100001300003
NC_000022.8Chr228301222290364

Samplesets

Number of Samplesets: 1

Size:
3
Organisms:
Homo sapiens
Sampleset Phenotype(s):
None reported
Sex:
Male
  • Download Samples as CSV file
  • Samples for sampleset 1
    Sample IDCell TypeSubject ID SexEthnicitySubject Phenotype
    YHYHMaleHan ChineseNot reported
    NA18507B-LymphocyteNA18507MaleYORUBANot reported
    JDWJDWMaleEuropeanNot reported

    Experimental Details

    Experiment IDTypeMethodAnalysisPlatformsDataNumber of Variant Calls
    1DiscoverySequencingRead depthIllumina Genome Analyzer and Roche/454 sequencer. For arrayCGH validation experiments we used NimblegenSRA, ftp://ftp.era-xml.ebi.ac.uk/vol1/ERA000/ERA000005/300
    2DiscoverySequencingRead depthIllumina Genome Analyzer and Roche/454 sequencer. For arrayCGH validation experiments we used NimblegenSRA, ftp://ftp.era-xml.ebi.ac.uk/vol1/ERA000/ERA000005/307
    3ValidationOligo aCGHProbe signal intensityGPL13934300
    4ValidationOligo aCGHProbe signal intensity307

    Validations

    Experiment IDMethodAnalysisPlatformNumber of Variant Calls Validated
    3Oligo aCGHProbe signal intensityGPL13934300
    4Oligo aCGHProbe signal intensity307
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