nstd175 (Genome in a Bottle)

Organism:
Human
Study Type:
Control Set
Submitter:
Justin Zook
Submitter version:
v0.6
Description:
The v0.6 Genome in a Bottle Consortium [www.genomeinabottle.org] structural variant (SV) benchmark set includes ~10,000 sequence-resolved insertions and deletions >49bp from the broadly-consented GIAB/Personal Genome Project Ashkenazi son (HG002/GM24385). These SVs, along with an accompanying benchmark BED file, are discovered and evaluated by multiple short, linked, and long read sequencing technologies and are intended as a benchmark for identifying false positive and false negative SV calls in any method. For more information, please refer to Zook, et al., bioRxiv (2019). Original VCF files and the benchmark BED file can be found here.
Project:
PRJNA200694

Detailed Information: Download 12745 Variant Regions, Download 12745 Variant Calls, Download Both, FTP

Variant Summary

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

Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.11Chr1951951RemappedNC_000001.11
NC_000002.12Chr2959959RemappedNC_000002.12
NC_000003.12Chr3745745RemappedNC_000003.12
NC_000004.12Chr4883883RemappedNC_000004.12
NC_000005.10Chr5689689RemappedNC_000005.10
NC_000006.12Chr6782782RemappedNC_000006.12
NC_000007.14Chr7768768RemappedNC_000007.14
NC_000008.11Chr8692692RemappedNC_000008.11
NC_000009.12Chr9506506RemappedNC_000009.12
NC_000010.11Chr10644644RemappedNC_000010.11
NC_000011.10Chr11593593RemappedNC_000011.10
NC_000012.12Chr12624624RemappedNC_000012.12
NC_000013.11Chr13525525RemappedNC_000013.11
NC_000014.9Chr14349349RemappedNC_000014.9
NC_000015.10Chr15312312RemappedNC_000015.10
NC_000016.10Chr16365365RemappedNC_000016.10
NC_000017.11Chr17438438RemappedNC_000017.11
NC_000018.10Chr18337337RemappedNC_000018.10
NC_000019.10Chr19404404RemappedNC_000019.10
NC_000020.11Chr20362362RemappedNC_000020.11
NC_000021.9Chr21228228RemappedNC_000021.9
NC_000022.11Chr22235235RemappedNC_000022.11
NC_000023.11ChrX297297RemappedNC_000023.11
NC_000024.10ChrY88RemappedNC_000024.10
NT_187515.1Chr1|NT_187515.155RemappedNT_187515.1
NT_187516.1Chr1|NT_187516.166RemappedNT_187516.1
NT_187518.1Chr1|NT_187518.122RemappedNT_187518.1
NT_187519.1Chr1|NT_187519.144RemappedNT_187519.1
NT_187646.1Chr1|NT_187646.122RemappedNT_187646.1
NW_003315907.2Chr1|NW_003315907.211RemappedNW_003315907.2
NW_009646194.1Chr1|NW_009646194.122RemappedNW_009646194.1
NW_009646196.1Chr1|NW_009646196.111RemappedNW_009646196.1
NW_011332687.1Chr1|NW_011332687.122RemappedNW_011332687.1
NW_011332688.1Chr1|NW_011332688.122RemappedNW_011332688.1
NW_014040925.1Chr1|NW_014040925.111RemappedNW_014040925.1
NW_014040926.1Chr1|NW_014040926.122RemappedNW_014040926.1
NW_014040927.1Chr1|NW_014040927.122RemappedNW_014040927.1
NW_017852928.1Chr1|NW_017852928.122RemappedNW_017852928.1
NW_018654706.1Chr1|NW_018654706.111RemappedNW_018654706.1
NW_019805487.1Chr1|NW_019805487.111RemappedNW_019805487.1
NT_187522.1Chr2|NT_187522.122RemappedNT_187522.1
NT_187523.1Chr2|NT_187523.133RemappedNT_187523.1
NT_187525.1Chr2|NT_187525.144RemappedNT_187525.1
NT_187526.1Chr2|NT_187526.111RemappedNT_187526.1
NT_187527.1Chr2|NT_187527.144RemappedNT_187527.1
NT_187529.1Chr2|NT_187529.155RemappedNT_187529.1
NT_187531.1Chr2|NT_187531.111RemappedNT_187531.1
NT_187647.1Chr2|NT_187647.133RemappedNT_187647.1
NW_003315908.1Chr2|NW_003315908.122RemappedNW_003315908.1
NW_003315909.1Chr2|NW_003315909.111RemappedNW_003315909.1
NW_011332689.1Chr2|NW_011332689.133RemappedNW_011332689.1
NW_011332690.1Chr2|NW_011332690.144RemappedNW_011332690.1
NW_015495299.1Chr2|NW_015495299.133RemappedNW_015495299.1
NW_018654710.1Chr2|NW_018654710.111RemappedNW_018654710.1
NT_187678.1Chr3|NT_187678.155RemappedNT_187678.1
NT_187688.1Chr3|NT_187688.155RemappedNT_187688.1
NT_187689.1Chr3|NT_187689.177RemappedNT_187689.1
NT_187690.1Chr3|NT_187690.144RemappedNT_187690.1
NT_187691.1Chr3|NT_187691.144RemappedNT_187691.1
NT_187532.1Chr3|NT_187532.177RemappedNT_187532.1
NT_187533.1Chr3|NT_187533.111RemappedNT_187533.1
NT_187534.1Chr3|NT_187534.111RemappedNT_187534.1
NT_187538.1Chr3|NT_187538.111RemappedNT_187538.1
NT_187649.1Chr3|NT_187649.155RemappedNT_187649.1
NW_003871060.2Chr3|NW_003871060.211RemappedNW_003871060.2
NW_009646197.1Chr3|NW_009646197.133RemappedNW_009646197.1
NW_011332691.1Chr3|NW_011332691.111RemappedNW_011332691.1
NW_012132916.1Chr3|NW_012132916.122RemappedNW_012132916.1
NW_017363813.1Chr3|NW_017363813.122RemappedNW_017363813.1
NW_018654711.1Chr3|NW_018654711.111RemappedNW_018654711.1
NW_019805488.1Chr3|NW_019805488.122RemappedNW_019805488.1
NW_019805489.1Chr3|NW_019805489.122RemappedNW_019805489.1
NW_019805490.1Chr3|NW_019805490.111RemappedNW_019805490.1
NW_019805492.1Chr3|NW_019805492.122RemappedNW_019805492.1
NT_187679.1Chr4|NT_187679.11212RemappedNT_187679.1
NT_187540.1Chr4|NT_187540.133RemappedNT_187540.1
NT_187541.1Chr4|NT_187541.122RemappedNT_187541.1
NT_187542.1Chr4|NT_187542.122RemappedNT_187542.1
NT_187543.1Chr4|NT_187543.144RemappedNT_187543.1
NT_187544.1Chr4|NT_187544.111RemappedNT_187544.1
NT_187545.1Chr4|NT_187545.133RemappedNT_187545.1
NT_187650.1Chr4|NT_187650.144RemappedNT_187650.1
NW_003315914.1Chr4|NW_003315914.111RemappedNW_003315914.1
NW_003315915.1Chr4|NW_003315915.111RemappedNW_003315915.1
NW_013171801.1Chr4|NW_013171801.122RemappedNW_013171801.1
NW_017363814.1Chr4|NW_017363814.122RemappedNW_017363814.1
NT_187546.1Chr5|NT_187546.122RemappedNT_187546.1
NT_187547.1Chr5|NT_187547.144RemappedNT_187547.1
NT_187548.1Chr5|NT_187548.155RemappedNT_187548.1
NT_187549.1Chr5|NT_187549.111RemappedNT_187549.1
NT_187550.1Chr5|NT_187550.144RemappedNT_187550.1
NT_187651.1Chr5|NT_187651.111RemappedNT_187651.1
NT_187652.1Chr5|NT_187652.133RemappedNT_187652.1
NW_003315917.2Chr5|NW_003315917.233RemappedNW_003315917.2
NW_003315918.1Chr5|NW_003315918.111RemappedNW_003315918.1
NW_003315920.1Chr5|NW_003315920.122RemappedNW_003315920.1
NW_016107297.1Chr5|NW_016107297.133RemappedNW_016107297.1
NW_016107298.1Chr5|NW_016107298.177RemappedNW_016107298.1
NT_187552.1Chr6|NT_187552.133RemappedNT_187552.1
NT_187553.1Chr6|NT_187553.155RemappedNT_187553.1
NT_187555.1Chr6|NT_187555.111RemappedNT_187555.1
NT_187556.1Chr6|NT_187556.111RemappedNT_187556.1
NT_187557.1Chr6|NT_187557.111RemappedNT_187557.1
NW_003315921.1Chr6|NW_003315921.111RemappedNW_003315921.1
NW_004166862.2Chr6|NW_004166862.21010RemappedNW_004166862.2
NW_009646200.1Chr6|NW_009646200.111RemappedNW_009646200.1
NW_012132918.1Chr6|NW_012132918.122RemappedNW_012132918.1
NW_013171802.1Chr6|NW_013171802.122RemappedNW_013171802.1
NW_017363815.1Chr6|NW_017363815.111RemappedNW_017363815.1
NW_018654713.1Chr6|NW_018654713.111RemappedNW_018654713.1
NT_187558.1Chr7|NT_187558.144RemappedNT_187558.1
NT_187560.1Chr7|NT_187560.11818RemappedNT_187560.1
NT_187562.1Chr7|NT_187562.122RemappedNT_187562.1
NT_187563.1Chr7|NT_187563.122RemappedNT_187563.1
NT_187564.1Chr7|NT_187564.122RemappedNT_187564.1
NT_187653.1Chr7|NT_187653.166RemappedNT_187653.1
NW_012132919.1Chr7|NW_012132919.111RemappedNW_012132919.1
NW_018654715.1Chr7|NW_018654715.111RemappedNW_018654715.1
NW_019805493.1Chr7|NW_019805493.111RemappedNW_019805493.1
NT_187680.1Chr8|NT_187680.166RemappedNT_187680.1
NT_187565.1Chr8|NT_187565.12121RemappedNT_187565.1
NT_187567.1Chr8|NT_187567.122RemappedNT_187567.1
NT_187568.1Chr8|NT_187568.11515RemappedNT_187568.1
NT_187569.1Chr8|NT_187569.122RemappedNT_187569.1
NT_187571.1Chr8|NT_187571.111RemappedNT_187571.1
NT_187572.1Chr8|NT_187572.155RemappedNT_187572.1
NT_187573.1Chr8|NT_187573.122RemappedNT_187573.1
NT_187574.1Chr8|NT_187574.166RemappedNT_187574.1
NT_187576.1Chr8|NT_187576.11717RemappedNT_187576.1
NT_187577.1Chr8|NT_187577.144RemappedNT_187577.1
NT_187654.1Chr8|NT_187654.11313RemappedNT_187654.1
NT_187655.1Chr8|NT_187655.133RemappedNT_187655.1
NW_017852931.1Chr8|NW_017852931.111RemappedNW_017852931.1
NW_018654716.1Chr8|NW_018654716.177RemappedNW_018654716.1
NW_018654717.1Chr8|NW_018654717.12727RemappedNW_018654717.1
NT_187578.1Chr9|NT_187578.111RemappedNT_187578.1
NW_003315931.1Chr9|NW_003315931.111RemappedNW_003315931.1
NW_009646201.1Chr9|NW_009646201.133RemappedNW_009646201.1
NW_013171804.1Chr9|NW_013171804.111RemappedNW_013171804.1
NW_003315934.1Chr10|NW_003315934.122RemappedNW_003315934.1
NW_003315935.1Chr10|NW_003315935.111RemappedNW_003315935.1
NT_187681.1Chr11|NT_187681.166RemappedNT_187681.1
NT_187656.1Chr11|NT_187656.144RemappedNT_187656.1
NT_187657.1Chr11|NT_187657.133RemappedNT_187657.1
NT_187581.1Chr11|NT_187581.144RemappedNT_187581.1
NT_187582.1Chr11|NT_187582.122RemappedNT_187582.1
NT_187583.1Chr11|NT_187583.111RemappedNT_187583.1
NT_187584.1Chr11|NT_187584.133RemappedNT_187584.1
NT_187585.1Chr11|NT_187585.111RemappedNT_187585.1
NT_187586.1Chr11|NT_187586.177RemappedNT_187586.1
NW_003315936.1Chr11|NW_003315936.122RemappedNW_003315936.1
NW_003871073.1Chr11|NW_003871073.111RemappedNW_003871073.1
NW_003871074.1Chr11|NW_003871074.111RemappedNW_003871074.1
NW_011332695.1Chr11|NW_011332695.111RemappedNW_011332695.1
NW_015148966.1Chr11|NW_015148966.166RemappedNW_015148966.1
NW_019805496.1Chr11|NW_019805496.122RemappedNW_019805496.1
NW_019805497.1Chr11|NW_019805497.122RemappedNW_019805497.1
NT_187658.1Chr12|NT_187658.144RemappedNT_187658.1
NT_187589.1Chr12|NT_187589.122RemappedNT_187589.1
NT_187590.1Chr12|NT_187590.111RemappedNT_187590.1
NT_187591.1Chr12|NT_187591.111RemappedNT_187591.1
NW_003315938.1Chr12|NW_003315938.111RemappedNW_003315938.1
NW_003315939.2Chr12|NW_003315939.222RemappedNW_003315939.2
NW_003315940.1Chr12|NW_003315940.133RemappedNW_003315940.1
NW_003571049.1Chr12|NW_003571049.122RemappedNW_003571049.1
NW_003571050.1Chr12|NW_003571050.144RemappedNW_003571050.1
NW_011332696.1Chr12|NW_011332696.133RemappedNW_011332696.1
NW_013171809.1Chr12|NW_013171809.122RemappedNW_013171809.1
NW_018654718.1Chr12|NW_018654718.188RemappedNW_018654718.1
NW_018654720.1Chr12|NW_018654720.133RemappedNW_018654720.1
NW_019805499.1Chr12|NW_019805499.111RemappedNW_019805499.1
NT_187592.1Chr13|NT_187592.122RemappedNT_187592.1
NT_187595.1Chr13|NT_187595.133RemappedNT_187595.1
NT_187596.1Chr13|NT_187596.144RemappedNT_187596.1
NT_187597.1Chr13|NT_187597.111RemappedNT_187597.1
NW_009646205.1Chr13|NW_009646205.111RemappedNW_009646205.1
NW_011332698.1Chr13|NW_011332698.11313RemappedNW_011332698.1
NW_011332700.1Chr13|NW_011332700.122RemappedNW_011332700.1
NW_013171811.1Chr13|NW_013171811.111RemappedNW_013171811.1
NT_187598.1Chr14|NT_187598.144RemappedNT_187598.1
NT_187599.1Chr14|NT_187599.122RemappedNT_187599.1
NT_187600.1Chr14|NT_187600.155RemappedNT_187600.1
NT_187601.1Chr14|NT_187601.166RemappedNT_187601.1
NW_018654721.1Chr14|NW_018654721.111RemappedNW_018654721.1
NW_018654722.1Chr14|NW_018654722.166RemappedNW_018654722.1
NT_187660.1Chr15|NT_187660.166RemappedNT_187660.1
NT_187603.1Chr15|NT_187603.111RemappedNT_187603.1
NT_187606.1Chr15|NT_187606.111RemappedNT_187606.1
NW_003315944.2Chr15|NW_003315944.222RemappedNW_003315944.2
NW_011332701.1Chr15|NW_011332701.166RemappedNW_011332701.1
NT_187607.1Chr16|NT_187607.133RemappedNT_187607.1
NT_187608.1Chr16|NT_187608.111RemappedNT_187608.1
NT_187610.1Chr16|NT_187610.155RemappedNT_187610.1
NW_003315946.1Chr16|NW_003315946.111RemappedNW_003315946.1
NW_012132921.1Chr16|NW_012132921.111RemappedNW_012132921.1
NW_013171812.1Chr16|NW_013171812.111RemappedNW_013171812.1
NW_013171813.1Chr16|NW_013171813.111RemappedNW_013171813.1
NW_017852933.1Chr16|NW_017852933.133RemappedNW_017852933.1
NW_019805500.1Chr16|NW_019805500.133RemappedNW_019805500.1
NT_187662.1Chr17|NT_187662.11313RemappedNT_187662.1
NT_187664.1Chr17|NT_187664.166RemappedNT_187664.1
NW_003871093.1Chr17|NW_003871093.111RemappedNW_003871093.1
NT_187611.1Chr17|NT_187611.122RemappedNT_187611.1
NT_187612.1Chr17|NT_187612.199RemappedNT_187612.1
NT_187613.1Chr17|NT_187613.11111RemappedNT_187613.1
NT_187614.1Chr17|NT_187614.11010RemappedNT_187614.1
NT_187615.1Chr17|NT_187615.111RemappedNT_187615.1
NT_187616.1Chr17|NT_187616.122RemappedNT_187616.1
NW_003315952.3Chr17|NW_003315952.31616RemappedNW_003315952.3
NW_003315954.1Chr17|NW_003315954.111RemappedNW_003315954.1
NW_003315955.1Chr17|NW_003315955.122RemappedNW_003315955.1
NW_003871091.1Chr17|NW_003871091.133RemappedNW_003871091.1
NW_017363817.1Chr17|NW_017363817.11010RemappedNW_017363817.1
NW_017363818.1Chr17|NW_017363818.111RemappedNW_017363818.1
NW_017363819.1Chr17|NW_017363819.122RemappedNW_017363819.1
NW_019805501.1Chr17|NW_019805501.122RemappedNW_019805501.1
NT_187665.1Chr18|NT_187665.166RemappedNT_187665.1
NT_187666.1Chr18|NT_187666.166RemappedNT_187666.1
NT_187617.1Chr18|NT_187617.144RemappedNT_187617.1
NW_003315956.1Chr18|NW_003315956.111RemappedNW_003315956.1
NW_003315957.1Chr18|NW_003315957.111RemappedNW_003315957.1
NW_003315958.1Chr18|NW_003315958.166RemappedNW_003315958.1
NW_003315959.1Chr18|NW_003315959.111RemappedNW_003315959.1
NW_003315960.1Chr18|NW_003315960.111RemappedNW_003315960.1
NW_003315961.1Chr18|NW_003315961.177RemappedNW_003315961.1
NW_013171814.1Chr18|NW_013171814.155RemappedNW_013171814.1
NW_014040928.1Chr18|NW_014040928.111RemappedNW_014040928.1
NW_018654724.1Chr18|NW_018654724.111RemappedNW_018654724.1
NW_019805503.1Chr18|NW_019805503.111RemappedNW_019805503.1
NT_187693.1Chr19|NT_187693.11515RemappedNT_187693.1
NW_003571061.2Chr19|NW_003571061.21010RemappedNW_003571061.2
NW_003571057.2Chr19|NW_003571057.299RemappedNW_003571057.2
NW_003571058.2Chr19|NW_003571058.299RemappedNW_003571058.2
NW_003571059.2Chr19|NW_003571059.299RemappedNW_003571059.2
NW_003571060.1Chr19|NW_003571060.11212RemappedNW_003571060.1
NW_003571056.2Chr19|NW_003571056.299RemappedNW_003571056.2
NW_003571055.2Chr19|NW_003571055.21212RemappedNW_003571055.2
NT_187622.1Chr19|NT_187622.155RemappedNT_187622.1
NW_003315962.1Chr19|NW_003315962.111RemappedNW_003315962.1
NW_003315963.1Chr19|NW_003315963.111RemappedNW_003315963.1
NW_003315964.2Chr19|NW_003315964.211RemappedNW_003315964.2
NW_003315965.1Chr19|NW_003315965.111RemappedNW_003315965.1
NW_003571054.1Chr19|NW_003571054.199RemappedNW_003571054.1
NW_009646206.1Chr19|NW_009646206.111RemappedNW_009646206.1
NW_014040929.1Chr19|NW_014040929.155RemappedNW_014040929.1
NT_187623.1Chr20|NT_187623.177RemappedNT_187623.1
NT_187624.1Chr20|NT_187624.166RemappedNT_187624.1
NT_187625.1Chr20|NT_187625.122RemappedNT_187625.1
NW_003315966.2Chr20|NW_003315966.211RemappedNW_003315966.2
NT_187626.1Chr21|NT_187626.166RemappedNT_187626.1
NT_187627.1Chr21|NT_187627.122RemappedNT_187627.1
NT_187628.1Chr21|NT_187628.122RemappedNT_187628.1
NW_003315968.2Chr21|NW_003315968.222RemappedNW_003315968.2
NW_003315969.2Chr21|NW_003315969.222RemappedNW_003315969.2
NT_187629.1Chr22|NT_187629.111RemappedNT_187629.1
NT_187630.1Chr22|NT_187630.111RemappedNT_187630.1
NT_187631.1Chr22|NT_187631.122RemappedNT_187631.1
NW_017363820.1ChrX|NW_017363820.111RemappedNW_017363820.1
NT_187635.1ChrX|NT_187635.111RemappedNT_187635.1
NW_009646209.1ChrY|NW_009646209.111RemappedNW_009646209.1
Sequence IDChrNumber of Variant RegionsNumber of Variant CallsPlacement typeLink to graphical display
NC_000001.10Chr1953953SubmittedNC_000001.10
NC_000002.11Chr2961961SubmittedNC_000002.11
NC_000003.11Chr3746746SubmittedNC_000003.11
NC_000004.11Chr4884884SubmittedNC_000004.11
NC_000005.9Chr5689689SubmittedNC_000005.9
NC_000006.11Chr6783783SubmittedNC_000006.11
NC_000007.13Chr7770770SubmittedNC_000007.13
NC_000008.10Chr8698698SubmittedNC_000008.10
NC_000009.11Chr9507507SubmittedNC_000009.11
NC_000010.10Chr10645645SubmittedNC_000010.10
NC_000011.9Chr11594594SubmittedNC_000011.9
NC_000012.11Chr12625625SubmittedNC_000012.11
NC_000013.10Chr13526526SubmittedNC_000013.10
NC_000014.8Chr14354354SubmittedNC_000014.8
NC_000015.9Chr15312312SubmittedNC_000015.9
NC_000016.9Chr16365365SubmittedNC_000016.9
NC_000017.10Chr17443443SubmittedNC_000017.10
NC_000018.9Chr18337337SubmittedNC_000018.9
NC_000019.9Chr19412412SubmittedNC_000019.9
NC_000020.10Chr20363363SubmittedNC_000020.10
NC_000021.8Chr21229229SubmittedNC_000021.8
NC_000022.10Chr22238238SubmittedNC_000022.10
NC_000023.10ChrX303303SubmittedNC_000023.10
NC_000024.9ChrY88SubmittedNC_000024.9

Variant Region remap statusVariant Call remap status
Sequence IDChrVariant Regions on sourcePerfectGoodPassFailMultVariant Calls on sourcePerfectGoodPassFailMult
NC_000001.10Chr19539131323495391313234
NC_000002.11Chr29619232023496192320234
NC_000003.11Chr37467180012774671800127
NC_000004.11Chr48848531012988485310129
NC_000005.9Chr56896560003368965600033
NC_000006.11Chr67837530012978375300129
NC_000007.13Chr77707320323377073203233
NC_000008.10Chr8698577003118698577003118
NC_000009.11Chr950750200055075020005
NC_000010.10Chr1064564001136456400113
NC_000011.9Chr115945580013559455800135
NC_000012.11Chr126255901013362559010133
NC_000013.10Chr135265000002652650000026
NC_000014.8Chr143543251142335432511423
NC_000015.9Chr153123020001031230200010
NC_000016.9Chr163653460001936534600019
NC_000017.10Chr174433730016944337300169
NC_000018.9Chr183373080002933730800029
NC_000019.9Chr194123790132941237901329
NC_000020.10Chr203633451011636334510116
NC_000021.8Chr212292140011422921400114
NC_000022.10Chr2223823010342382301034
NC_000023.10ChrX30329500623032950062
NC_000024.9ChrY870001870001

Samplesets

Number of Samplesets: 1

Name:
HG002
Size:
1
Organisms:
Homo sapiens
Sampleset Phenotype(s):
None reported
  • Download Samples as CSV file
  • Samples for sampleset 1
    Sample IDSubject ID SexSubject Phenotype
    SAMN03283347GM24385MaleNot reported

    Experimental Details

    Experiment IDTypeMethodAnalysisNumber of Variant Calls
    1DiscoverySequencingSequence alignment12,745

    Validations

    No validation data were submitted for this study.

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