nstd206 (Byrska-Bishop et al. 2021)

Organism:
Human
Study Type:
Collection
Submitter:
Uday S Evani
Description:
The 1000 Genomes Project (1kGP), launched in 2008, is the largest fully open resource of whole genome sequencing (WGS) data consented for public distribution of raw sequence data without access or use restrictions. Here, we present a new, ​high coverage WGS resource encompassing the original 2,504 1kGP samples, as well as an additional 698 related samples that result in 602 complete trios in the 1kGP cohort. We sequenced this expanded 1kGP cohort of 3,202 samples to a targeted depth of 30X using Illumina NovaSeq 6000 instruments. We performed SNV/INDEL calling against the GRCh38 reference using GATK’s HaplotypeCaller, and generated a comprehensive set of SVs by integrating multiple analytic methods through a sophisticated machine learning model, upgrading the 1kGP dataset to current state-of-the-art standards. We called 7% more SNVs, 59% more INDELs, and 170% more SVs per genome than the phase 3 callset. Moreover, we leveraged the presence of families in the cohort to achieve superior haplotype phasing accuracy and we demonstrate improvements that the high coverage panel brings especially for INDEL imputation. We make all the data generated as part of this project publicly available and we envision this updated version of the 1kGP callset to become the new de facto public resource for the worldwide scientific community working on genomics and genetics. See Variant Summary counts for nstd206 in dbVar Variant Summary.

Detailed Information: Download 170211 Variant Regions, Download 170226 Variant Calls, Download Both, FTP

Variant Summary

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

Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.11Chr112,89812,900SubmittedNC_000001.11
NC_000002.12Chr213,51013,511SubmittedNC_000002.12
NC_000003.12Chr311,06011,060SubmittedNC_000003.12
NC_000004.12Chr411,05511,058SubmittedNC_000004.12
NC_000005.10Chr510,21810,219SubmittedNC_000005.10
NC_000006.12Chr69,9219,922SubmittedNC_000006.12
NC_000007.14Chr710,47110,472SubmittedNC_000007.14
NC_000008.11Chr88,3748,374SubmittedNC_000008.11
NC_000009.12Chr97,0587,058SubmittedNC_000009.12
NC_000010.11Chr107,7507,751SubmittedNC_000010.11
NC_000011.10Chr118,1148,114SubmittedNC_000011.10
NC_000012.12Chr128,1318,131SubmittedNC_000012.12
NC_000013.11Chr135,7765,776SubmittedNC_000013.11
NC_000014.9Chr145,5595,560SubmittedNC_000014.9
NC_000015.10Chr154,7604,761SubmittedNC_000015.10
NC_000016.10Chr165,2065,207SubmittedNC_000016.10
NC_000017.11Chr175,4795,480SubmittedNC_000017.11
NC_000018.10Chr184,5454,545SubmittedNC_000018.10
NC_000019.10Chr195,1395,139SubmittedNC_000019.10
NC_000020.11Chr203,7283,728SubmittedNC_000020.11
NC_000021.9Chr212,3282,328SubmittedNC_000021.9
NC_000022.11Chr222,4352,435SubmittedNC_000022.11
NC_000023.11ChrX6,3566,357SubmittedNC_000023.11
NC_000024.10ChrY340340SubmittedNC_000024.10
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.10Chr112,66112,662RemappedNC_000001.10
NC_000002.11Chr213,48413,485RemappedNC_000002.11
NC_000003.11Chr311,03811,038RemappedNC_000003.11
NC_000004.11Chr411,05311,056RemappedNC_000004.11
NC_000005.9Chr510,21710,218RemappedNC_000005.9
NC_000006.11Chr69,8319,832RemappedNC_000006.11
NC_000007.13Chr710,28810,289RemappedNC_000007.13
NC_000008.10Chr88,2958,295RemappedNC_000008.10
NC_000009.11Chr96,9556,955RemappedNC_000009.11
NC_000010.10Chr107,6237,624RemappedNC_000010.10
NC_000011.9Chr118,0908,090RemappedNC_000011.9
NC_000012.11Chr128,1198,119RemappedNC_000012.11
NC_000013.10Chr135,7505,750RemappedNC_000013.10
NC_000014.8Chr145,3135,314RemappedNC_000014.8
NC_000015.9Chr154,7534,754RemappedNC_000015.9
NC_000016.9Chr165,0705,071RemappedNC_000016.9
NC_000017.10Chr175,2805,281RemappedNC_000017.10
NC_000018.9Chr184,5324,532RemappedNC_000018.9
NC_000019.9Chr194,9694,969RemappedNC_000019.9
NC_000020.10Chr203,6183,618RemappedNC_000020.10
NC_000021.8Chr212,2512,251RemappedNC_000021.8
NC_000022.10Chr222,3132,313RemappedNC_000022.10
NC_000023.10ChrX6,2766,277RemappedNC_000023.10
NC_000024.9ChrY313313RemappedNC_000024.9
NT_113923.1Unplaced|NT_113923.133RemappedNT_113923.1
NT_167216.1Unplaced|NT_167216.122RemappedNT_167216.1
NT_167222.1Unplaced|NT_167222.111RemappedNT_167222.1
NT_167227.1Unplaced|NT_167227.144RemappedNT_167227.1
NT_167214.1Unplaced|NT_167214.122RemappedNT_167214.1
NT_167218.1Unplaced|NT_167218.133RemappedNT_167218.1
NT_167225.1Unplaced|NT_167225.133RemappedNT_167225.1
NT_167226.1Unplaced|NT_167226.111RemappedNT_167226.1
NT_167229.1Unplaced|NT_167229.133RemappedNT_167229.1
NT_167211.1Unplaced|NT_167211.155RemappedNT_167211.1
NT_167223.1Unplaced|NT_167223.111RemappedNT_167223.1
NT_167228.1Unplaced|NT_167228.111RemappedNT_167228.1
NT_167233.1Unplaced|NT_167233.133RemappedNT_167233.1
NT_167237.1Unplaced|NT_167237.111RemappedNT_167237.1
NT_167209.1Unplaced|NT_167209.111RemappedNT_167209.1
NT_167207.1Chr1|NT_167207.12323RemappedNT_167207.1
NW_003315903.1Chr1|NW_003315903.177RemappedNW_003315903.1
NW_003315904.1Chr1|NW_003315904.155RemappedNW_003315904.1
NW_003571030.1Chr1|NW_003571030.11010RemappedNW_003571030.1
NW_003871055.3Chr1|NW_003871055.3431432RemappedNW_003871055.3
NW_003871056.3Chr1|NW_003871056.34949RemappedNW_003871056.3
NW_003871057.1Chr1|NW_003871057.13030RemappedNW_003871057.1
NW_004070863.1Chr1|NW_004070863.144RemappedNW_004070863.1
NW_004070864.2Chr1|NW_004070864.222RemappedNW_004070864.2
NW_004070865.1Chr1|NW_004070865.11010RemappedNW_004070865.1
NW_003571031.1Chr2|NW_003571031.155RemappedNW_003571031.1
NW_003571032.1Chr2|NW_003571032.111RemappedNW_003571032.1
NW_004504299.1Chr2|NW_004504299.12626RemappedNW_004504299.1
NW_003315910.1Chr3|NW_003315910.188RemappedNW_003315910.1
NW_003315911.1Chr3|NW_003315911.144RemappedNW_003315911.1
NW_003315912.1Chr3|NW_003315912.133RemappedNW_003315912.1
NW_003871058.1Chr3|NW_003871058.12424RemappedNW_003871058.1
NW_003871059.1Chr3|NW_003871059.199RemappedNW_003871059.1
NW_003871060.1Chr3|NW_003871060.144RemappedNW_003871060.1
NW_004775426.1Chr3|NW_004775426.11111RemappedNW_004775426.1
NT_113885.1Chr4|NT_113885.199RemappedNT_113885.1
NT_113888.1Chr4|NT_113888.111RemappedNT_113888.1
NT_167250.1Chr4|NT_167250.111RemappedNT_167250.1
NW_003315916.1Chr4|NW_003315916.155RemappedNW_003315916.1
NW_003571034.1Chr4|NW_003571034.11818RemappedNW_003571034.1
NW_003571035.1Chr4|NW_003571035.11313RemappedNW_003571035.1
NW_004775427.1Chr4|NW_004775427.17272RemappedNW_004775427.1
NW_003871061.1Chr5|NW_003871061.11313RemappedNW_003871061.1
NW_004775428.1Chr5|NW_004775428.13636RemappedNW_004775428.1
NT_167246.1Chr6|NT_167246.177RemappedNT_167246.1
NT_167248.1Chr6|NT_167248.177RemappedNT_167248.1
NT_167249.1Chr6|NT_167249.111RemappedNT_167249.1
NW_003871062.1Chr6|NW_003871062.11414RemappedNW_003871062.1
NW_004070866.1Chr6|NW_004070866.11414RemappedNW_004070866.1
NW_004504300.1Chr6|NW_004504300.13838RemappedNW_004504300.1
NW_004775429.1Chr6|NW_004775429.188RemappedNW_004775429.1
NW_003571037.1Chr7|NW_003571037.12828RemappedNW_003571037.1
NW_003571038.1Chr7|NW_003571038.11818RemappedNW_003571038.1
NW_003571039.1Chr7|NW_003571039.12929RemappedNW_003571039.1
NW_003571040.1Chr7|NW_003571040.14949RemappedNW_003571040.1
NW_003571041.1Chr7|NW_003571041.11414RemappedNW_003571041.1
NW_003871064.1Chr7|NW_003871064.1262262RemappedNW_003871064.1
NW_003871065.1Chr7|NW_003871065.12525RemappedNW_003871065.1
NW_004775430.1Chr7|NW_004775430.13131RemappedNW_004775430.1
NW_003315923.1Chr8|NW_003315923.15454RemappedNW_003315923.1
NW_003315924.1Chr8|NW_003315924.11717RemappedNW_003315924.1
NW_003571042.1Chr8|NW_003571042.15454RemappedNW_003571042.1
NW_003871066.2Chr8|NW_003871066.233RemappedNW_003871066.2
NW_004775431.1Chr8|NW_004775431.11414RemappedNW_004775431.1
NT_113914.1Chr9|NT_113914.155RemappedNT_113914.1
NT_113916.2Chr9|NT_113916.22121RemappedNT_113916.2
NW_003315925.1Chr9|NW_003315925.13535RemappedNW_003315925.1
NW_003315926.1Chr9|NW_003315926.133RemappedNW_003315926.1
NW_003315927.1Chr9|NW_003315927.177RemappedNW_003315927.1
NW_003871067.1Chr9|NW_003871067.188RemappedNW_003871067.1
NW_004070867.1Chr9|NW_004070867.133RemappedNW_004070867.1
NW_004070868.1Chr9|NW_004070868.11717RemappedNW_004070868.1
NW_004070869.1Chr9|NW_004070869.11414RemappedNW_004070869.1
NW_004504301.1Chr9|NW_004504301.11414RemappedNW_004504301.1
NW_003315932.1Chr10|NW_003315932.12525RemappedNW_003315932.1
NW_003315933.1Chr10|NW_003315933.144RemappedNW_003315933.1
NW_003571043.1Chr10|NW_003571043.11414RemappedNW_003571043.1
NW_003871068.1Chr10|NW_003871068.1135135RemappedNW_003871068.1
NW_003871069.1Chr10|NW_003871069.188RemappedNW_003871069.1
NW_003871070.1Chr10|NW_003871070.166RemappedNW_003871070.1
NW_003871071.1Chr10|NW_003871071.13232RemappedNW_003871071.1
NW_004070870.1Chr10|NW_004070870.11515RemappedNW_004070870.1
NW_004504302.1Chr10|NW_004504302.12929RemappedNW_004504302.1
NW_004775432.1Chr10|NW_004775432.15151RemappedNW_004775432.1
NT_113921.2Chr11|NT_113921.233RemappedNT_113921.2
NW_003571045.1Chr11|NW_003571045.12222RemappedNW_003571045.1
NW_003571046.1Chr11|NW_003571046.11414RemappedNW_003571046.1
NW_003871072.2Chr11|NW_003871072.23232RemappedNW_003871072.2
NW_003871075.1Chr11|NW_003871075.11717RemappedNW_003871075.1
NW_003871076.1Chr11|NW_003871076.12121RemappedNW_003871076.1
NW_003871077.1Chr11|NW_003871077.188RemappedNW_003871077.1
NW_003871078.1Chr11|NW_003871078.11515RemappedNW_003871078.1
NW_003871079.1Chr11|NW_003871079.11818RemappedNW_003871079.1
NW_003871080.1Chr11|NW_003871080.11919RemappedNW_003871080.1
NW_003871081.1Chr11|NW_003871081.144RemappedNW_003871081.1
NW_003871082.1Chr11|NW_003871082.177RemappedNW_003871082.1
NW_004070871.1Chr11|NW_004070871.13333RemappedNW_004070871.1
NW_003315937.1Chr12|NW_003315937.12727RemappedNW_003315937.1
NW_003571048.1Chr12|NW_003571048.11919RemappedNW_003571048.1
NW_003871083.2Chr12|NW_003871083.22222RemappedNW_003871083.2
NW_004504303.2Chr12|NW_004504303.22929RemappedNW_004504303.2
NW_003571051.1Chr13|NW_003571051.188RemappedNW_003571051.1
NW_004166863.1Chr14|NW_004166863.1271271RemappedNW_004166863.1
NW_003871084.1Chr15|NW_003871084.11717RemappedNW_003871084.1
NW_003871085.1Chr16|NW_003871085.122RemappedNW_003871085.1
NT_113930.1Chr17|NT_113930.111RemappedNT_113930.1
NT_113941.1Chr17|NT_113941.111RemappedNT_113941.1
NT_113943.1Chr17|NT_113943.155RemappedNT_113943.1
NW_003315947.1Chr17|NW_003315947.13131RemappedNW_003315947.1
NW_003315948.2Chr17|NW_003315948.255RemappedNW_003315948.2
NW_003315949.1Chr17|NW_003315949.11616RemappedNW_003315949.1
NW_003315950.2Chr17|NW_003315950.27171RemappedNW_003315950.2
NW_003315951.1Chr17|NW_003315951.144RemappedNW_003315951.1
NW_003571052.1Chr17|NW_003571052.13030RemappedNW_003571052.1
NW_003871087.1Chr17|NW_003871087.11919RemappedNW_003871087.1
NW_003871088.1Chr17|NW_003871088.12525RemappedNW_003871088.1
NW_003871089.1Chr17|NW_003871089.12525RemappedNW_003871089.1
NW_003871090.1Chr17|NW_003871090.11414RemappedNW_003871090.1
NW_004070872.2Chr17|NW_004070872.27575RemappedNW_004070872.2
NW_004166864.2Chr17|NW_004166864.21111RemappedNW_004166864.2
NW_004775433.1Chr17|NW_004775433.188RemappedNW_004775433.1
NT_113947.1Chr18|NT_113947.111RemappedNT_113947.1
NW_003571053.2Chr19|NW_003571053.27575RemappedNW_003571053.2
NW_003871094.1Chr19|NW_003871094.11313RemappedNW_003871094.1
NW_004166865.1Chr19|NW_004166865.1150150RemappedNW_004166865.1
NW_004775434.1Chr19|NW_004775434.14646RemappedNW_004775434.1
NW_003571063.2Chr20|NW_003571063.21818RemappedNW_003571063.2
NW_003871095.1Chr20|NW_003871095.166RemappedNW_003871095.1
NW_004504304.1Chr20|NW_004504304.12626RemappedNW_004504304.1
NT_113950.2Chr21|NT_113950.211RemappedNT_113950.2
NW_003315968.1Chr21|NW_003315968.188RemappedNW_003315968.1
NW_004775435.1Chr21|NW_004775435.12424RemappedNW_004775435.1
NT_113961.1Chr22|NT_113961.11414RemappedNT_113961.1
NW_003315972.1Chr22|NW_003315972.111RemappedNW_003315972.1
NW_003871096.1Chr22|NW_003871096.12525RemappedNW_003871096.1
NW_004070875.1Chr22|NW_004070875.111RemappedNW_004070875.1
NW_004070876.1Chr22|NW_004070876.144RemappedNW_004070876.1
NT_167212.1Chr22|NT_167212.199RemappedNT_167212.1
NT_167234.1Chr22|NT_167234.111RemappedNT_167234.1
NT_167235.1Chr22|NT_167235.144RemappedNT_167235.1
NW_003571064.2ChrX|NW_003571064.29999RemappedNW_003571064.2
NW_003871098.1ChrX|NW_003871098.12828RemappedNW_003871098.1
NW_003871099.1ChrX|NW_003871099.11616RemappedNW_003871099.1
NW_003871100.1ChrX|NW_003871100.15858RemappedNW_003871100.1
NW_003871101.3ChrX|NW_003871101.32020RemappedNW_003871101.3
NW_003871102.1ChrX|NW_003871102.111RemappedNW_003871102.1
NW_003871103.3ChrX|NW_003871103.3182182RemappedNW_003871103.3
NW_004070877.1ChrX|NW_004070877.1159159RemappedNW_004070877.1
NW_004070878.1ChrX|NW_004070878.13232RemappedNW_004070878.1
NW_004070879.1ChrX|NW_004070879.11313RemappedNW_004070879.1
NW_004070880.2ChrX|NW_004070880.2108109RemappedNW_004070880.2
NW_004070881.1ChrX|NW_004070881.144RemappedNW_004070881.1
NW_004070882.1ChrX|NW_004070882.12525RemappedNW_004070882.1
NW_004070883.1ChrX|NW_004070883.11313RemappedNW_004070883.1
NW_004070884.1ChrX|NW_004070884.133RemappedNW_004070884.1
NW_004070885.1ChrX|NW_004070885.11616RemappedNW_004070885.1
NW_004070886.1ChrX|NW_004070886.11616RemappedNW_004070886.1
NW_004070887.1ChrX|NW_004070887.15555RemappedNW_004070887.1
NW_004070888.1ChrX|NW_004070888.13939RemappedNW_004070888.1
NW_004070889.1ChrX|NW_004070889.14545RemappedNW_004070889.1
NW_004070890.2ChrX|NW_004070890.2264264RemappedNW_004070890.2
NW_004070891.1ChrX|NW_004070891.15353RemappedNW_004070891.1
NW_004070892.1ChrX|NW_004070892.13939RemappedNW_004070892.1
NW_004070893.1ChrX|NW_004070893.155RemappedNW_004070893.1
NW_004166866.1ChrX|NW_004166866.12121RemappedNW_004166866.1

Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000001.11Chr112,89812,47853241832512,90012,480532418325
NC_000002.12Chr213,51013,3477624303313,51113,34876243033
NC_000003.12Chr311,06010,941467135311,06010,9414671353
NC_000004.12Chr411,05510,92720399611,05810,930203996
NC_000005.10Chr510,21810,14220254910,21910,143202549
NC_000006.12Chr69,9219,732371073699,9229,73337107369
NC_000007.14Chr710,4719,866783511038210,4729,8677835110382
NC_000008.11Chr88,3748,23444216698,3748,2344421669
NC_000009.12Chr97,0586,900101749827,0586,90010174982
NC_000010.11Chr107,7507,4592712232297,7517,460271223229
NC_000011.10Chr118,1147,8573111132028,1147,857311113202
NC_000012.12Chr128,1318,0111259948,1318,011125994
NC_000013.11Chr135,7765,739382155,7765,73938215
NC_000014.9Chr145,5595,44545345305,5605,4464534530
NC_000015.10Chr154,7604,68737127174,7614,6883712717
NC_000016.10Chr165,2065,003422113825,2075,00442211382
NC_000017.11Chr175,4795,2284923191605,4805,229492319160
NC_000018.10Chr184,5454,5161541004,5454,516154100
NC_000019.10Chr195,1394,9553513111255,1394,955351311125
NC_000020.11Chr203,7283,56530981433,7283,5653098143
NC_000021.9Chr212,3282,204441243252,3282,20444124325
NC_000022.11Chr222,4352,241862158282,4352,24186215828
NC_000023.11ChrX6,3564,9745828311,2656,3574,9745828311,266
NC_000024.10ChrY3402998132034029981320

Samplesets

Number of Samplesets: 1

Size:
3,202 (sample data not available)
Organisms:
Homo sapiens
Sampleset Phenotype(s):
None reported

Experimental Details

Experiment IDTypeMethodAnalysisNumber of Variant Calls
1DiscoverySequencingSequence alignment170,226

Validations

No validation data were submitted for this study.

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