nstd204 (Chen et al. 2021)

Organism:
Human
Study Type:
Collection
Submitter:
Lei Chen
Description:
Structural variation (SV) callsets were generated from whole genome sequencing data of 4,848 Finnish individuals and are composed of 129,166 high-confidence autosome SVs detected by three SV calling pipelines: LUMPY, GenomeSTRiP and CNVnator. All genomes were sequenced at >20x coverage on the Illumina HiSeq X or NovaSeq platforms with paired-end 150bp reads. In each callset, site-level SV data are available with frequency information. More information can be found at Chen et al., biorxiv (2020). See Variant Summary counts for nstd204 in dbVar Variant Summary.
Publication(s):
Chen et al. 2021

Detailed Information: Download 129165 Variant Regions, Download 129166 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_000001.11Chr111,19711,197SubmittedNC_000001.11
NC_000002.12Chr29,9939,993SubmittedNC_000002.12
NC_000003.12Chr36,4556,456SubmittedNC_000003.12
NC_000004.12Chr47,2577,257SubmittedNC_000004.12
NC_000005.10Chr57,1267,126SubmittedNC_000005.10
NC_000006.12Chr66,3146,314SubmittedNC_000006.12
NC_000007.14Chr78,2598,259SubmittedNC_000007.14
NC_000008.11Chr86,1756,175SubmittedNC_000008.11
NC_000009.12Chr99,0289,028SubmittedNC_000009.12
NC_000010.11Chr105,9995,999SubmittedNC_000010.11
NC_000011.10Chr115,4635,463SubmittedNC_000011.10
NC_000012.12Chr124,8544,854SubmittedNC_000012.12
NC_000013.11Chr134,0004,000SubmittedNC_000013.11
NC_000014.9Chr144,4574,457SubmittedNC_000014.9
NC_000015.10Chr155,8135,813SubmittedNC_000015.10
NC_000016.10Chr165,7025,702SubmittedNC_000016.10
NC_000017.11Chr175,3055,305SubmittedNC_000017.11
NC_000018.10Chr182,4492,449SubmittedNC_000018.10
NC_000019.10Chr194,1454,145SubmittedNC_000019.10
NC_000020.11Chr203,1743,174SubmittedNC_000020.11
NC_000021.9Chr212,3892,389SubmittedNC_000021.9
NC_000022.11Chr223,8933,893SubmittedNC_000022.11
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.10Chr19,8369,836RemappedNC_000001.10
NC_000002.11Chr29,8989,898RemappedNC_000002.11
NC_000003.11Chr36,3676,368RemappedNC_000003.11
NC_000004.11Chr47,2667,266RemappedNC_000004.11
NC_000005.9Chr57,0997,099RemappedNC_000005.9
NC_000006.11Chr66,2076,207RemappedNC_000006.11
NC_000007.13Chr77,8587,858RemappedNC_000007.13
NC_000008.10Chr86,0546,054RemappedNC_000008.10
NC_000009.11Chr99,0559,055RemappedNC_000009.11
NC_000010.10Chr105,2395,239RemappedNC_000010.10
NC_000011.9Chr115,4205,420RemappedNC_000011.9
NC_000012.11Chr124,7464,746RemappedNC_000012.11
NC_000013.10Chr133,7643,764RemappedNC_000013.10
NC_000014.8Chr144,0704,070RemappedNC_000014.8
NC_000015.9Chr155,7695,769RemappedNC_000015.9
NC_000016.9Chr165,7065,706RemappedNC_000016.9
NC_000017.10Chr174,4124,412RemappedNC_000017.10
NC_000018.9Chr182,4522,452RemappedNC_000018.9
NC_000019.9Chr193,8343,834RemappedNC_000019.9
NC_000020.10Chr202,3832,383RemappedNC_000020.10
NC_000021.8Chr212,2972,297RemappedNC_000021.8
NC_000022.10Chr222,7532,753RemappedNC_000022.10
NC_000024.9ChrY7777RemappedNC_000024.9
NT_113923.1Unplaced|NT_113923.1113113RemappedNT_113923.1
NT_167215.1Unplaced|NT_167215.11212RemappedNT_167215.1
NT_167216.1Unplaced|NT_167216.12727RemappedNT_167216.1
NT_167227.1Unplaced|NT_167227.177RemappedNT_167227.1
NT_113889.1Unplaced|NT_113889.111RemappedNT_113889.1
NT_167214.1Unplaced|NT_167214.12020RemappedNT_167214.1
NT_167218.1Unplaced|NT_167218.111RemappedNT_167218.1
NT_167213.1Unplaced|NT_167213.14141RemappedNT_167213.1
NT_167225.1Unplaced|NT_167225.11616RemappedNT_167225.1
NT_167226.1Unplaced|NT_167226.18888RemappedNT_167226.1
NT_167229.1Unplaced|NT_167229.13838RemappedNT_167229.1
NT_167230.1Unplaced|NT_167230.111RemappedNT_167230.1
NT_167211.1Unplaced|NT_167211.11111RemappedNT_167211.1
NT_167223.1Unplaced|NT_167223.133RemappedNT_167223.1
NT_167224.1Unplaced|NT_167224.177RemappedNT_167224.1
NT_167228.1Unplaced|NT_167228.11818RemappedNT_167228.1
NT_167231.1Unplaced|NT_167231.122RemappedNT_167231.1
NT_167233.1Unplaced|NT_167233.11111RemappedNT_167233.1
NT_167237.1Unplaced|NT_167237.166RemappedNT_167237.1
NT_167207.1Chr1|NT_167207.15656RemappedNT_167207.1
NW_003315903.1Chr1|NW_003315903.11212RemappedNW_003315903.1
NW_003315904.1Chr1|NW_003315904.188RemappedNW_003315904.1
NW_003571030.1Chr1|NW_003571030.199RemappedNW_003571030.1
NW_003871055.3Chr1|NW_003871055.31,6171,617RemappedNW_003871055.3
NW_003871056.3Chr1|NW_003871056.3567567RemappedNW_003871056.3
NW_003871057.1Chr1|NW_003871057.13131RemappedNW_003871057.1
NW_004070863.1Chr1|NW_004070863.133RemappedNW_004070863.1
NW_004070865.1Chr1|NW_004070865.144RemappedNW_004070865.1
NW_003571031.1Chr2|NW_003571031.12424RemappedNW_003571031.1
NW_003571032.1Chr2|NW_003571032.11313RemappedNW_003571032.1
NW_004504299.1Chr2|NW_004504299.12424RemappedNW_004504299.1
NW_003315910.1Chr3|NW_003315910.188RemappedNW_003315910.1
NW_003871058.1Chr3|NW_003871058.12222RemappedNW_003871058.1
NW_003871059.1Chr3|NW_003871059.166RemappedNW_003871059.1
NW_004775426.1Chr3|NW_004775426.133RemappedNW_004775426.1
NT_113885.1Chr4|NT_113885.12222RemappedNT_113885.1
NT_113888.1Chr4|NT_113888.15555RemappedNT_113888.1
NW_003315916.1Chr4|NW_003315916.111RemappedNW_003315916.1
NW_003571034.1Chr4|NW_003571034.1141141RemappedNW_003571034.1
NW_003571035.1Chr4|NW_003571035.11414RemappedNW_003571035.1
NW_004775427.1Chr4|NW_004775427.14242RemappedNW_004775427.1
NW_003871061.1Chr5|NW_003871061.144RemappedNW_003871061.1
NW_004775428.1Chr5|NW_004775428.15656RemappedNW_004775428.1
NT_167246.1Chr6|NT_167246.155RemappedNT_167246.1
NT_167248.1Chr6|NT_167248.155RemappedNT_167248.1
NT_167249.1Chr6|NT_167249.111RemappedNT_167249.1
NW_003871062.1Chr6|NW_003871062.111RemappedNW_003871062.1
NW_004070866.1Chr6|NW_004070866.17373RemappedNW_004070866.1
NW_004504300.1Chr6|NW_004504300.12020RemappedNW_004504300.1
NW_004775429.1Chr6|NW_004775429.11818RemappedNW_004775429.1
NT_113901.1Chr7|NT_113901.133RemappedNT_113901.1
NW_003571037.1Chr7|NW_003571037.11818RemappedNW_003571037.1
NW_003571038.1Chr7|NW_003571038.13333RemappedNW_003571038.1
NW_003571039.1Chr7|NW_003571039.1122122RemappedNW_003571039.1
NW_003571040.1Chr7|NW_003571040.17070RemappedNW_003571040.1
NW_003571041.1Chr7|NW_003571041.11111RemappedNW_003571041.1
NW_003871064.1Chr7|NW_003871064.1356356RemappedNW_003871064.1
NW_003871065.1Chr7|NW_003871065.11010RemappedNW_003871065.1
NW_004775430.1Chr7|NW_004775430.18686RemappedNW_004775430.1
NW_003315923.1Chr8|NW_003315923.13535RemappedNW_003315923.1
NW_003315924.1Chr8|NW_003315924.11414RemappedNW_003315924.1
NW_003571042.1Chr8|NW_003571042.18686RemappedNW_003571042.1
NW_003871066.2Chr8|NW_003871066.211RemappedNW_003871066.2
NW_004775431.1Chr8|NW_004775431.11212RemappedNW_004775431.1
NT_113914.1Chr9|NT_113914.13737RemappedNT_113914.1
NT_113915.1Chr9|NT_113915.199RemappedNT_113915.1
NT_113916.2Chr9|NT_113916.255RemappedNT_113916.2
NW_003315925.1Chr9|NW_003315925.11717RemappedNW_003315925.1
NW_003315926.1Chr9|NW_003315926.155RemappedNW_003315926.1
NW_003315927.1Chr9|NW_003315927.122RemappedNW_003315927.1
NW_003871067.1Chr9|NW_003871067.15252RemappedNW_003871067.1
NW_004070867.1Chr9|NW_004070867.122RemappedNW_004070867.1
NW_004070868.1Chr9|NW_004070868.11010RemappedNW_004070868.1
NW_004070869.1Chr9|NW_004070869.11919RemappedNW_004070869.1
NW_004504301.1Chr9|NW_004504301.133RemappedNW_004504301.1
NW_003315932.1Chr10|NW_003315932.155RemappedNW_003315932.1
NW_003315933.1Chr10|NW_003315933.122RemappedNW_003315933.1
NW_003571043.1Chr10|NW_003571043.13939RemappedNW_003571043.1
NW_003871068.1Chr10|NW_003871068.1954954RemappedNW_003871068.1
NW_003871069.1Chr10|NW_003871069.133RemappedNW_003871069.1
NW_003871070.1Chr10|NW_003871070.111RemappedNW_003871070.1
NW_003871071.1Chr10|NW_003871071.12424RemappedNW_003871071.1
NW_004070870.1Chr10|NW_004070870.11616RemappedNW_004070870.1
NW_004504302.1Chr10|NW_004504302.15656RemappedNW_004504302.1
NW_004775432.1Chr10|NW_004775432.14444RemappedNW_004775432.1
NT_113921.2Chr11|NT_113921.233RemappedNT_113921.2
NW_003571045.1Chr11|NW_003571045.12121RemappedNW_003571045.1
NW_003571046.1Chr11|NW_003571046.166RemappedNW_003571046.1
NW_003871072.2Chr11|NW_003871072.22222RemappedNW_003871072.2
NW_003871075.1Chr11|NW_003871075.155RemappedNW_003871075.1
NW_003871076.1Chr11|NW_003871076.11212RemappedNW_003871076.1
NW_003871077.1Chr11|NW_003871077.11111RemappedNW_003871077.1
NW_003871078.1Chr11|NW_003871078.144RemappedNW_003871078.1
NW_003871079.1Chr11|NW_003871079.133RemappedNW_003871079.1
NW_003871080.1Chr11|NW_003871080.155RemappedNW_003871080.1
NW_003871082.1Chr11|NW_003871082.155RemappedNW_003871082.1
NW_004070871.1Chr11|NW_004070871.177RemappedNW_004070871.1
NW_003315937.1Chr12|NW_003315937.13030RemappedNW_003315937.1
NW_003571048.1Chr12|NW_003571048.15050RemappedNW_003571048.1
NW_003871083.2Chr12|NW_003871083.299RemappedNW_003871083.2
NW_004504303.2Chr12|NW_004504303.22727RemappedNW_004504303.2
NW_003571051.1Chr13|NW_003571051.155RemappedNW_003571051.1
NW_004166863.1Chr14|NW_004166863.1422422RemappedNW_004166863.1
NW_003871084.1Chr15|NW_003871084.12222RemappedNW_003871084.1
NW_003871085.1Chr16|NW_003871085.122RemappedNW_003871085.1
NT_113930.1Chr17|NT_113930.12929RemappedNT_113930.1
NT_113941.1Chr17|NT_113941.133RemappedNT_113941.1
NT_113943.1Chr17|NT_113943.111RemappedNT_113943.1
NW_003315947.1Chr17|NW_003315947.11919RemappedNW_003315947.1
NW_003315948.2Chr17|NW_003315948.211RemappedNW_003315948.2
NW_003315949.1Chr17|NW_003315949.1462462RemappedNW_003315949.1
NW_003315950.2Chr17|NW_003315950.2284284RemappedNW_003315950.2
NW_003315951.1Chr17|NW_003315951.144RemappedNW_003315951.1
NW_003571052.1Chr17|NW_003571052.188RemappedNW_003571052.1
NW_003871087.1Chr17|NW_003871087.12929RemappedNW_003871087.1
NW_003871088.1Chr17|NW_003871088.12626RemappedNW_003871088.1
NW_003871089.1Chr17|NW_003871089.11111RemappedNW_003871089.1
NW_003871090.1Chr17|NW_003871090.11414RemappedNW_003871090.1
NW_004070872.2Chr17|NW_004070872.29797RemappedNW_004070872.2
NW_004166864.2Chr17|NW_004166864.233RemappedNW_004166864.2
NW_004775433.1Chr17|NW_004775433.18888RemappedNW_004775433.1
NT_113947.1Chr18|NT_113947.111RemappedNT_113947.1
NW_003571053.2Chr19|NW_003571053.25959RemappedNW_003571053.2
NW_003871094.1Chr19|NW_003871094.14646RemappedNW_003871094.1
NW_004166865.1Chr19|NW_004166865.1298298RemappedNW_004166865.1
NW_004775434.1Chr19|NW_004775434.12525RemappedNW_004775434.1
NW_003571063.2Chr20|NW_003571063.299RemappedNW_003571063.2
NW_004504304.1Chr20|NW_004504304.11212RemappedNW_004504304.1
NW_003315968.1Chr21|NW_003315968.155RemappedNW_003315968.1
NW_004775435.1Chr21|NW_004775435.166RemappedNW_004775435.1
NT_113961.1Chr22|NT_113961.12828RemappedNT_113961.1
NW_003871096.1Chr22|NW_003871096.12222RemappedNW_003871096.1
NW_004070873.1Chr22|NW_004070873.13838RemappedNW_004070873.1
NW_004070874.1Chr22|NW_004070874.13030RemappedNW_004070874.1
NW_004070875.1Chr22|NW_004070875.11212RemappedNW_004070875.1
NW_004070876.1Chr22|NW_004070876.122RemappedNW_004070876.1
NT_167212.1Chr22|NT_167212.1285285RemappedNT_167212.1
NT_167234.1Chr22|NT_167234.14747RemappedNT_167234.1
NT_167235.1Chr22|NT_167235.17171RemappedNT_167235.1
NT_167238.1Chr22|NT_167238.199RemappedNT_167238.1

Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000001.11Chr111,1979,4003061531272,18711,1979,4003061531272,187
NC_000002.12Chr29,9939,12827587901,4339,9939,12827587901,433
NC_000003.12Chr36,4555,90481271211,1296,4565,90581271211,129
NC_000004.12Chr47,2576,79640591,3117,2576,79640591,311
NC_000005.10Chr57,1266,730251321,1547,1266,730251321,154
NC_000006.12Chr66,3145,78749281061,0996,3145,78749281061,099
NC_000007.14Chr78,2597,0632201071221,4498,2597,0632201071221,449
NC_000008.11Chr86,1755,7359636229776,1755,735963622977
NC_000009.12Chr99,0288,269228148868819,0288,26922814886881
NC_000010.11Chr105,9994,902152391411,3215,9994,902152391411,321
NC_000011.10Chr115,4635,0484715409635,4635,048471540963
NC_000012.12Chr124,8544,412481129594,8544,41248112959
NC_000013.11Chr134,0003,68727231426874,0003,6872723142687
NC_000014.9Chr144,4573,963144112216504,4573,96314411221650
NC_000015.10Chr155,8135,19433260456305,8135,1943326045630
NC_000016.10Chr165,7025,295108541174915,7025,29510854117491
NC_000017.11Chr175,3054,56531075496635,3054,5653107549663
NC_000018.10Chr182,4492,3021311314182,4492,302131131418
NC_000019.10Chr194,1453,8433811145564,1453,843381114556
NC_000020.11Chr203,1742,1863512193035033,1742,186351219303503
NC_000021.9Chr212,3892,11210641402932,3892,1121064140293
NC_000022.11Chr223,8932,9215601521363473,8932,921560152136347

Samplesets

Number of Samplesets: 1

Sampleset Type:
Control
Size:
4,848 (sample data not available)
Organisms:
Homo sapiens
Sampleset Phenotype(s):
None reported

Experimental Details

Experiment IDTypeMethodAnalysisNumber of Variant Calls
1DiscoverySequencingSplit read and paired-end mapping35,713
2DiscoverySequencingRead depth39,660
3DiscoverySequencingRead depth53,793

Validations

No validation data were submitted for this study.

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