nstd209 (Almarri et al. 2020)

Organism:
Human
Study Type:
Control Set
Submitter:
Mohamed A Almarri
Description:
Structural variants contribute substantially to genetic diversity and are important evolutionarily and medically, but they are still understudied. Here we present a comprehensive analysis of structural variation in the Human Genome Diversity panel, a high-coverage dataset of 911 samples from 54 diverse worldwide populations. We identify, in total, 126,018 variants, 78% of which were not identified in previous global sequencing projects. Some reach high frequency and are private to continental groups or even individual populations, including regionally restricted runaway duplications and putatively introgressed variants from archaic hominins. By de novo assembly of 25 genomes using linked-read sequencing, we discover 1,643 breakpoint-resolved unique insertions, in aggregate accounting for 1.9 Mb of sequence absent from the GRCh38 reference. Our results illustrate the limitation of a single human reference and the need for high-quality genomes from diverse populations to fully discover and understand human genetic variation. See Variant Summary counts for nstd209 in dbVar Variant Summary.
Publication(s):
Almarri et al. 2020

Detailed Information: Download 152814 Variant Regions, Download 167799 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_000001.11Chr110,68011,738SubmittedNC_000001.11
NC_000002.12Chr211,06511,981SubmittedNC_000002.12
NC_000003.12Chr39,60310,508SubmittedNC_000003.12
NC_000004.12Chr49,42710,153SubmittedNC_000004.12
NC_000005.10Chr59,2199,972SubmittedNC_000005.10
NC_000006.12Chr68,3028,860SubmittedNC_000006.12
NC_000007.14Chr79,32910,385SubmittedNC_000007.14
NC_000008.11Chr87,1427,853SubmittedNC_000008.11
NC_000009.12Chr97,7348,778SubmittedNC_000009.12
NC_000010.11Chr106,4356,956SubmittedNC_000010.11
NC_000011.10Chr117,1567,820SubmittedNC_000011.10
NC_000012.12Chr128,6179,557SubmittedNC_000012.12
NC_000013.11Chr135,5416,083SubmittedNC_000013.11
NC_000014.9Chr145,3415,879SubmittedNC_000014.9
NC_000015.10Chr154,2164,847SubmittedNC_000015.10
NC_000016.10Chr165,1545,862SubmittedNC_000016.10
NC_000017.11Chr175,0705,631SubmittedNC_000017.11
NC_000018.10Chr183,6953,965SubmittedNC_000018.10
NC_000019.10Chr195,0375,489SubmittedNC_000019.10
NC_000020.11Chr203,6223,844SubmittedNC_000020.11
NC_000021.9Chr212,0322,223SubmittedNC_000021.9
NC_000022.11Chr222,6843,040SubmittedNC_000022.11
NC_000023.11ChrX5,3265,794SubmittedNC_000023.11
NC_000024.10ChrY387581SubmittedNC_000024.10
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.10Chr110,32611,298RemappedNC_000001.10
NC_000002.11Chr210,95011,867RemappedNC_000002.11
NC_000003.11Chr39,31710,146RemappedNC_000003.11
NC_000004.11Chr49,42110,152RemappedNC_000004.11
NC_000005.9Chr59,0769,830RemappedNC_000005.9
NC_000006.11Chr68,2408,862RemappedNC_000006.11
NC_000007.13Chr79,03510,034RemappedNC_000007.13
NC_000008.10Chr87,0407,732RemappedNC_000008.10
NC_000009.11Chr97,6508,700RemappedNC_000009.11
NC_000010.10Chr106,0996,539RemappedNC_000010.10
NC_000011.9Chr117,0747,736RemappedNC_000011.9
NC_000012.11Chr128,3979,331RemappedNC_000012.11
NC_000013.10Chr135,3075,801RemappedNC_000013.10
NC_000014.8Chr144,7385,210RemappedNC_000014.8
NC_000015.9Chr154,1734,804RemappedNC_000015.9
NC_000016.9Chr165,0515,746RemappedNC_000016.9
NC_000017.10Chr174,6975,130RemappedNC_000017.10
NC_000018.9Chr183,6223,889RemappedNC_000018.9
NC_000019.9Chr194,8505,261RemappedNC_000019.9
NC_000020.10Chr203,1453,314RemappedNC_000020.10
NC_000021.8Chr212,0042,200RemappedNC_000021.8
NC_000022.10Chr222,4762,733RemappedNC_000022.10
NC_000023.10ChrX5,2245,682RemappedNC_000023.10
NC_000024.9ChrY389582RemappedNC_000024.9
NT_113923.1Unplaced|NT_113923.14995RemappedNT_113923.1
NT_167216.1Unplaced|NT_167216.169RemappedNT_167216.1
NT_167227.1Unplaced|NT_167227.158RemappedNT_167227.1
NT_167213.1Unplaced|NT_167213.12228RemappedNT_167213.1
NT_167225.1Unplaced|NT_167225.11523RemappedNT_167225.1
NT_167226.1Unplaced|NT_167226.11720RemappedNT_167226.1
NT_167229.1Unplaced|NT_167229.122RemappedNT_167229.1
NT_167211.1Unplaced|NT_167211.133RemappedNT_167211.1
NT_167223.1Unplaced|NT_167223.1710RemappedNT_167223.1
NT_167224.1Unplaced|NT_167224.1611RemappedNT_167224.1
NT_167228.1Unplaced|NT_167228.1714RemappedNT_167228.1
NT_167231.1Unplaced|NT_167231.111RemappedNT_167231.1
NT_167237.1Unplaced|NT_167237.111RemappedNT_167237.1
NT_167207.1Chr1|NT_167207.179RemappedNT_167207.1
NW_003315903.1Chr1|NW_003315903.11929RemappedNW_003315903.1
NW_003315904.1Chr1|NW_003315904.11617RemappedNW_003315904.1
NW_003571030.1Chr1|NW_003571030.199RemappedNW_003571030.1
NW_003871055.3Chr1|NW_003871055.3339471RemappedNW_003871055.3
NW_003871056.3Chr1|NW_003871056.34867RemappedNW_003871056.3
NW_003871057.1Chr1|NW_003871057.11618RemappedNW_003871057.1
NW_004070863.1Chr1|NW_004070863.122RemappedNW_004070863.1
NW_004070864.2Chr1|NW_004070864.255RemappedNW_004070864.2
NW_004070865.1Chr1|NW_004070865.111RemappedNW_004070865.1
NW_003571031.1Chr2|NW_003571031.124RemappedNW_003571031.1
NW_003571032.1Chr2|NW_003571032.11718RemappedNW_003571032.1
NW_004504299.1Chr2|NW_004504299.11717RemappedNW_004504299.1
NW_003315910.1Chr3|NW_003315910.133RemappedNW_003315910.1
NW_003315911.1Chr3|NW_003315911.122RemappedNW_003315911.1
NW_003315912.1Chr3|NW_003315912.111RemappedNW_003315912.1
NW_003871058.1Chr3|NW_003871058.12834RemappedNW_003871058.1
NW_003871059.1Chr3|NW_003871059.133RemappedNW_003871059.1
NW_003871060.1Chr3|NW_003871060.166RemappedNW_003871060.1
NW_004775426.1Chr3|NW_004775426.11212RemappedNW_004775426.1
NT_113885.1Chr4|NT_113885.177RemappedNT_113885.1
NW_003315916.1Chr4|NW_003315916.145RemappedNW_003315916.1
NW_003571034.1Chr4|NW_003571034.11520RemappedNW_003571034.1
NW_003571035.1Chr4|NW_003571035.11111RemappedNW_003571035.1
NW_004775427.1Chr4|NW_004775427.1103148RemappedNW_004775427.1
NW_003871061.1Chr5|NW_003871061.199RemappedNW_003871061.1
NW_004775428.1Chr5|NW_004775428.12637RemappedNW_004775428.1
NT_167249.1Chr6|NT_167249.111RemappedNT_167249.1
NW_003871062.1Chr6|NW_003871062.177RemappedNW_003871062.1
NW_004070866.1Chr6|NW_004070866.11825RemappedNW_004070866.1
NW_004504300.1Chr6|NW_004504300.13435RemappedNW_004504300.1
NW_004775429.1Chr6|NW_004775429.177RemappedNW_004775429.1
NW_003571037.1Chr7|NW_003571037.12627RemappedNW_003571037.1
NW_003571038.1Chr7|NW_003571038.11919RemappedNW_003571038.1
NW_003571039.1Chr7|NW_003571039.12939RemappedNW_003571039.1
NW_003571040.1Chr7|NW_003571040.18294RemappedNW_003571040.1
NW_003571041.1Chr7|NW_003571041.11819RemappedNW_003571041.1
NW_003871064.1Chr7|NW_003871064.1285359RemappedNW_003871064.1
NW_003871065.1Chr7|NW_003871065.12529RemappedNW_003871065.1
NW_004775430.1Chr7|NW_004775430.12228RemappedNW_004775430.1
NW_003315923.1Chr8|NW_003315923.12425RemappedNW_003315923.1
NW_003315924.1Chr8|NW_003315924.12424RemappedNW_003315924.1
NW_003571042.1Chr8|NW_003571042.16179RemappedNW_003571042.1
NW_003871066.2Chr8|NW_003871066.244RemappedNW_003871066.2
NW_004775431.1Chr8|NW_004775431.11619RemappedNW_004775431.1
NT_113914.1Chr9|NT_113914.145RemappedNT_113914.1
NT_113915.1Chr9|NT_113915.124RemappedNT_113915.1
NT_113916.2Chr9|NT_113916.21212RemappedNT_113916.2
NW_003315925.1Chr9|NW_003315925.17377RemappedNW_003315925.1
NW_003315926.1Chr9|NW_003315926.199RemappedNW_003315926.1
NW_003315927.1Chr9|NW_003315927.188RemappedNW_003315927.1
NW_003871067.1Chr9|NW_003871067.169RemappedNW_003871067.1
NW_004070867.1Chr9|NW_004070867.188RemappedNW_004070867.1
NW_004070868.1Chr9|NW_004070868.11719RemappedNW_004070868.1
NW_004070869.1Chr9|NW_004070869.16263RemappedNW_004070869.1
NW_004504301.1Chr9|NW_004504301.166RemappedNW_004504301.1
NW_003315932.1Chr10|NW_003315932.11819RemappedNW_003315932.1
NW_003315933.1Chr10|NW_003315933.156RemappedNW_003315933.1
NW_003571043.1Chr10|NW_003571043.14467RemappedNW_003571043.1
NW_003871068.1Chr10|NW_003871068.1160280RemappedNW_003871068.1
NW_003871069.1Chr10|NW_003871069.199RemappedNW_003871069.1
NW_003871070.1Chr10|NW_003871070.122RemappedNW_003871070.1
NW_003871071.1Chr10|NW_003871071.14047RemappedNW_003871071.1
NW_004070870.1Chr10|NW_004070870.188RemappedNW_004070870.1
NW_004504302.1Chr10|NW_004504302.12222RemappedNW_004504302.1
NW_004775432.1Chr10|NW_004775432.12828RemappedNW_004775432.1
NT_113921.2Chr11|NT_113921.211RemappedNT_113921.2
NW_003571045.1Chr11|NW_003571045.12326RemappedNW_003571045.1
NW_003571046.1Chr11|NW_003571046.11414RemappedNW_003571046.1
NW_003871072.2Chr11|NW_003871072.22528RemappedNW_003871072.2
NW_003871075.1Chr11|NW_003871075.11414RemappedNW_003871075.1
NW_003871076.1Chr11|NW_003871076.11212RemappedNW_003871076.1
NW_003871077.1Chr11|NW_003871077.166RemappedNW_003871077.1
NW_003871078.1Chr11|NW_003871078.11111RemappedNW_003871078.1
NW_003871079.1Chr11|NW_003871079.177RemappedNW_003871079.1
NW_003871080.1Chr11|NW_003871080.188RemappedNW_003871080.1
NW_003871081.1Chr11|NW_003871081.122RemappedNW_003871081.1
NW_003871082.1Chr11|NW_003871082.199RemappedNW_003871082.1
NW_004070871.1Chr11|NW_004070871.13939RemappedNW_004070871.1
NW_003315937.1Chr12|NW_003315937.15860RemappedNW_003315937.1
NW_003571048.1Chr12|NW_003571048.14650RemappedNW_003571048.1
NW_003871083.2Chr12|NW_003871083.288RemappedNW_003871083.2
NW_004504303.2Chr12|NW_004504303.22831RemappedNW_004504303.2
NW_003571051.1Chr13|NW_003571051.11617RemappedNW_003571051.1
NW_004166863.1Chr14|NW_004166863.1622697RemappedNW_004166863.1
NW_003871084.1Chr15|NW_003871084.12121RemappedNW_003871084.1
NW_003871085.1Chr16|NW_003871085.133RemappedNW_003871085.1
NT_113930.1Chr17|NT_113930.111RemappedNT_113930.1
NT_113943.1Chr17|NT_113943.133RemappedNT_113943.1
NW_003315947.1Chr17|NW_003315947.11717RemappedNW_003315947.1
NW_003315948.2Chr17|NW_003315948.2910RemappedNW_003315948.2
NW_003315949.1Chr17|NW_003315949.12591RemappedNW_003315949.1
NW_003315950.2Chr17|NW_003315950.2109161RemappedNW_003315950.2
NW_003315951.1Chr17|NW_003315951.11011RemappedNW_003315951.1
NW_003571052.1Chr17|NW_003571052.11818RemappedNW_003571052.1
NW_003871087.1Chr17|NW_003871087.12020RemappedNW_003871087.1
NW_003871088.1Chr17|NW_003871088.12930RemappedNW_003871088.1
NW_003871089.1Chr17|NW_003871089.12828RemappedNW_003871089.1
NW_003871090.1Chr17|NW_003871090.188RemappedNW_003871090.1
NW_004070872.2Chr17|NW_004070872.2114141RemappedNW_004070872.2
NW_004166864.2Chr17|NW_004166864.255RemappedNW_004166864.2
NW_004775433.1Chr17|NW_004775433.17592RemappedNW_004775433.1
NW_003571053.2Chr19|NW_003571053.26071RemappedNW_003571053.2
NW_003871094.1Chr19|NW_003871094.13542RemappedNW_003871094.1
NW_004166865.1Chr19|NW_004166865.1177221RemappedNW_004166865.1
NW_004775434.1Chr19|NW_004775434.13738RemappedNW_004775434.1
NW_003571063.2Chr20|NW_003571063.22932RemappedNW_003571063.2
NW_003871095.1Chr20|NW_003871095.122RemappedNW_003871095.1
NW_004504304.1Chr20|NW_004504304.11919RemappedNW_004504304.1
NW_003315968.1Chr21|NW_003315968.188RemappedNW_003315968.1
NW_004775435.1Chr21|NW_004775435.13335RemappedNW_004775435.1
NT_113961.1Chr22|NT_113961.12753RemappedNT_113961.1
NW_003871096.1Chr22|NW_003871096.12224RemappedNW_003871096.1
NW_004070873.1Chr22|NW_004070873.111RemappedNW_004070873.1
NW_004070874.1Chr22|NW_004070874.11026RemappedNW_004070874.1
NW_004070875.1Chr22|NW_004070875.122RemappedNW_004070875.1
NW_004070876.1Chr22|NW_004070876.144RemappedNW_004070876.1
NT_167212.1Chr22|NT_167212.12037RemappedNT_167212.1
NT_167234.1Chr22|NT_167234.133RemappedNT_167234.1
NT_167235.1Chr22|NT_167235.13249RemappedNT_167235.1
NW_003571064.2ChrX|NW_003571064.2159189RemappedNW_003571064.2
NW_003871098.1ChrX|NW_003871098.12626RemappedNW_003871098.1
NW_003871099.1ChrX|NW_003871099.11213RemappedNW_003871099.1
NW_003871100.1ChrX|NW_003871100.13737RemappedNW_003871100.1
NW_003871101.3ChrX|NW_003871101.31010RemappedNW_003871101.3
NW_003871102.1ChrX|NW_003871102.111RemappedNW_003871102.1
NW_003871103.3ChrX|NW_003871103.3181218RemappedNW_003871103.3
NW_004070877.1ChrX|NW_004070877.1104115RemappedNW_004070877.1
NW_004070878.1ChrX|NW_004070878.11616RemappedNW_004070878.1
NW_004070879.1ChrX|NW_004070879.199RemappedNW_004070879.1
NW_004070880.2ChrX|NW_004070880.26878RemappedNW_004070880.2
NW_004070881.1ChrX|NW_004070881.13655RemappedNW_004070881.1
NW_004070882.1ChrX|NW_004070882.12021RemappedNW_004070882.1
NW_004070883.1ChrX|NW_004070883.155RemappedNW_004070883.1
NW_004070884.1ChrX|NW_004070884.133RemappedNW_004070884.1
NW_004070885.1ChrX|NW_004070885.11622RemappedNW_004070885.1
NW_004070886.1ChrX|NW_004070886.11515RemappedNW_004070886.1
NW_004070887.1ChrX|NW_004070887.13039RemappedNW_004070887.1
NW_004070888.1ChrX|NW_004070888.12843RemappedNW_004070888.1
NW_004070889.1ChrX|NW_004070889.12020RemappedNW_004070889.1
NW_004070890.2ChrX|NW_004070890.2200204RemappedNW_004070890.2
NW_004070891.1ChrX|NW_004070891.14848RemappedNW_004070891.1
NW_004070892.1ChrX|NW_004070892.12121RemappedNW_004070892.1
NW_004070893.1ChrX|NW_004070893.122RemappedNW_004070893.1
NW_004166866.1ChrX|NW_004166866.11010RemappedNW_004166866.1

Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000001.11Chr110,68010,077893121127211,73810,98314443220348
NC_000002.12Chr211,06510,654217441183211,98111,5082625412235
NC_000003.12Chr39,6039,220102322034610,50810,0241705320952
NC_000004.12Chr49,4279,2522732212310,1539,92136322171
NC_000005.10Chr59,2199,013201150359,9729,74926115046
NC_000006.12Chr68,3028,0456322119538,8608,575792512259
NC_000007.14Chr79,3298,5191977313340710,3859,37827992140496
NC_000008.11Chr87,1426,969692327547,8537,65091262858
NC_000009.12Chr97,7347,4474424631568,7788,446693268163
NC_000010.11Chr106,4355,9351292342456,9566,3801210236318
NC_000011.10Chr117,1566,886258741637,8207,54125976169
NC_000012.12Chr128,6178,24617142031379,5579,1691917206146
NC_000013.11Chr135,5415,33566181136,0835,8736918213
NC_000014.9Chr145,3414,95116118711315,8795,4551751941243
NC_000015.10Chr154,2164,12323544214,8474,7245164521
NC_000016.10Chr165,1544,858895914355,8625,482139771595
NC_000017.11Chr175,0704,7197921791725,6315,1971054081208
NC_000018.10Chr183,6953,6041357303,9653,866178740
NC_000019.10Chr195,0374,850403111335,4895,27743311155
NC_000020.11Chr203,6223,0958552344463,8443,2571156735748
NC_000021.9Chr212,0321,94329621332,2232,1303162135
NC_000022.11Chr222,6842,2902673563293,0402,542346546731
NC_000023.11ChrX5,3264,1914614501,0255,7944,5066016521,160
NC_000024.10ChrY3873733011058156330150

Samplesets

Number of Samplesets: 1

Name:
Human Genome Diversity Panel
Description:
A high-coverage dataset of 911 samples from 54 diverse worldwide populations.
Size:
914 (sample data not available)
Organisms:
Homo sapiens
Sampleset Phenotype(s):
None reported

Experimental Details

Experiment IDTypeMethodAnalysisNumber of Variant Calls
1DiscoverySequencingSequence alignment167,799

Validations

No validation data were submitted for this study.

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