nstd152 (Chaisson et al. 2019)
- Organism:
- Human
- Study Type:
- Collection
- Submitter:
- Mark Chaisson
- Description:
- This is an integrated callset from three individuals (HG00514, HG00733, and NA19240) sequenced using Illumina, Illumina 3.5 kbp jumping libraries, Illumina 6kbp jumping libraries, PacBio, BioNano Genomics, 10x, Hi-C, and Strand-seq. See Variant Summary counts for nstd152 in dbVar Variant Summary.
- Publication(s):
- Chaisson et al. 2019
Detailed Information: Download 103985 Variant Regions, Download 214917 Variant Calls, Download Both, FTP
Variant Summary
Assembly used for analysis:
Submitted: GRCh38 (hg38)
Remapped: GRCh37.p13 (hg19)
| Sequence ID | Chr | Number of Variant Regions | Number of Variant Calls | Placement type | Link to graphical display |
|---|---|---|---|---|---|
| NC_000001.11 | Chr1 | 7,395 | 15,661 | Submitted | NC_000001.11 |
| NC_000002.12 | Chr2 | 7,206 | 15,055 | Submitted | NC_000002.12 |
| NC_000003.12 | Chr3 | 5,523 | 11,489 | Submitted | NC_000003.12 |
| NC_000004.12 | Chr4 | 6,561 | 14,022 | Submitted | NC_000004.12 |
| NC_000005.10 | Chr5 | 5,800 | 11,833 | Submitted | NC_000005.10 |
| NC_000006.12 | Chr6 | 6,267 | 13,533 | Submitted | NC_000006.12 |
| NC_000007.14 | Chr7 | 6,462 | 13,313 | Submitted | NC_000007.14 |
| NC_000008.11 | Chr8 | 5,175 | 10,661 | Submitted | NC_000008.11 |
| NC_000009.12 | Chr9 | 4,339 | 9,548 | Submitted | NC_000009.12 |
| NC_000010.11 | Chr10 | 4,947 | 10,068 | Submitted | NC_000010.11 |
| NC_000011.10 | Chr11 | 4,829 | 10,061 | Submitted | NC_000011.10 |
| NC_000012.12 | Chr12 | 5,048 | 10,213 | Submitted | NC_000012.12 |
| NC_000013.11 | Chr13 | 3,654 | 7,797 | Submitted | NC_000013.11 |
| NC_000014.9 | Chr14 | 2,746 | 5,728 | Submitted | NC_000014.9 |
| NC_000015.10 | Chr15 | 2,562 | 5,387 | Submitted | NC_000015.10 |
| NC_000016.10 | Chr16 | 3,589 | 6,788 | Submitted | NC_000016.10 |
| NC_000017.11 | Chr17 | 3,894 | 7,515 | Submitted | NC_000017.11 |
| NC_000018.10 | Chr18 | 3,008 | 5,963 | Submitted | NC_000018.10 |
| NC_000019.10 | Chr19 | 3,621 | 7,020 | Submitted | NC_000019.10 |
| NC_000020.11 | Chr20 | 2,809 | 5,672 | Submitted | NC_000020.11 |
| NC_000021.9 | Chr21 | 2,159 | 4,448 | Submitted | NC_000021.9 |
| NC_000022.11 | Chr22 | 2,302 | 4,637 | Submitted | NC_000022.11 |
| NC_000023.11 | ChrX | 4,052 | 8,454 | Submitted | NC_000023.11 |
| NC_000024.10 | ChrY | 37 | 51 | Submitted | NC_000024.10 |
| Sequence ID | Chr | Number of Variant Regions | Number of Variant Calls | Placement type | Link to graphical display |
|---|---|---|---|---|---|
| NC_000001.10 | Chr1 | 7,194 | 15,298 | Remapped | NC_000001.10 |
| NC_000002.11 | Chr2 | 7,123 | 14,871 | Remapped | NC_000002.11 |
| NC_000003.11 | Chr3 | 5,470 | 11,380 | Remapped | NC_000003.11 |
| NC_000004.11 | Chr4 | 6,519 | 13,899 | Remapped | NC_000004.11 |
| NC_000005.9 | Chr5 | 5,786 | 11,785 | Remapped | NC_000005.9 |
| NC_000006.11 | Chr6 | 6,091 | 13,158 | Remapped | NC_000006.11 |
| NC_000007.13 | Chr7 | 6,353 | 13,074 | Remapped | NC_000007.13 |
| NC_000008.10 | Chr8 | 5,024 | 10,429 | Remapped | NC_000008.10 |
| NC_000009.11 | Chr9 | 4,249 | 9,316 | Remapped | NC_000009.11 |
| NC_000010.10 | Chr10 | 4,751 | 9,643 | Remapped | NC_000010.10 |
| NC_000011.9 | Chr11 | 4,766 | 9,936 | Remapped | NC_000011.9 |
| NC_000012.11 | Chr12 | 4,976 | 10,056 | Remapped | NC_000012.11 |
| NC_000013.10 | Chr13 | 3,616 | 7,712 | Remapped | NC_000013.10 |
| NC_000014.8 | Chr14 | 2,652 | 5,530 | Remapped | NC_000014.8 |
| NC_000015.9 | Chr15 | 2,532 | 5,328 | Remapped | NC_000015.9 |
| NC_000016.9 | Chr16 | 3,538 | 6,693 | Remapped | NC_000016.9 |
| NC_000017.10 | Chr17 | 3,443 | 6,725 | Remapped | NC_000017.10 |
| NC_000018.9 | Chr18 | 2,960 | 5,858 | Remapped | NC_000018.9 |
| NC_000019.9 | Chr19 | 3,432 | 6,654 | Remapped | NC_000019.9 |
| NC_000020.10 | Chr20 | 2,686 | 5,416 | Remapped | NC_000020.10 |
| NC_000021.8 | Chr21 | 2,009 | 4,156 | Remapped | NC_000021.8 |
| NC_000022.10 | Chr22 | 2,071 | 4,006 | Remapped | NC_000022.10 |
| NC_000023.10 | ChrX | 3,871 | 8,009 | Remapped | NC_000023.10 |
| NC_000024.9 | ChrY | 41 | 65 | Remapped | NC_000024.9 |
| NT_113923.1 | Unplaced|NT_113923.1 | 13 | 29 | Remapped | NT_113923.1 |
| NT_167216.1 | Unplaced|NT_167216.1 | 2 | 5 | Remapped | NT_167216.1 |
| NT_167222.1 | Unplaced|NT_167222.1 | 14 | 15 | Remapped | NT_167222.1 |
| NT_167227.1 | Unplaced|NT_167227.1 | 6 | 6 | Remapped | NT_167227.1 |
| NT_167214.1 | Unplaced|NT_167214.1 | 8 | 18 | Remapped | NT_167214.1 |
| NT_167213.1 | Unplaced|NT_167213.1 | 2 | 18 | Remapped | NT_167213.1 |
| NT_167225.1 | Unplaced|NT_167225.1 | 6 | 23 | Remapped | NT_167225.1 |
| NT_167226.1 | Unplaced|NT_167226.1 | 9 | 24 | Remapped | NT_167226.1 |
| NT_167229.1 | Unplaced|NT_167229.1 | 5 | 21 | Remapped | NT_167229.1 |
| NT_167230.1 | Unplaced|NT_167230.1 | 1 | 2 | Remapped | NT_167230.1 |
| NT_167211.1 | Unplaced|NT_167211.1 | 9 | 27 | Remapped | NT_167211.1 |
| NT_167223.1 | Unplaced|NT_167223.1 | 1 | 1 | Remapped | NT_167223.1 |
| NT_167228.1 | Unplaced|NT_167228.1 | 2 | 18 | Remapped | NT_167228.1 |
| NT_167233.1 | Unplaced|NT_167233.1 | 3 | 7 | Remapped | NT_167233.1 |
| NT_167237.1 | Unplaced|NT_167237.1 | 3 | 3 | Remapped | NT_167237.1 |
| NT_167209.1 | Unplaced|NT_167209.1 | 3 | 4 | Remapped | NT_167209.1 |
| NT_167207.1 | Chr1|NT_167207.1 | 11 | 18 | Remapped | NT_167207.1 |
| NW_003315903.1 | Chr1|NW_003315903.1 | 14 | 18 | Remapped | NW_003315903.1 |
| NW_003315904.1 | Chr1|NW_003315904.1 | 14 | 18 | Remapped | NW_003315904.1 |
| NW_003571030.1 | Chr1|NW_003571030.1 | 13 | 29 | Remapped | NW_003571030.1 |
| NW_003871055.3 | Chr1|NW_003871055.3 | 212 | 456 | Remapped | NW_003871055.3 |
| NW_003871056.3 | Chr1|NW_003871056.3 | 57 | 128 | Remapped | NW_003871056.3 |
| NW_003871057.1 | Chr1|NW_003871057.1 | 15 | 30 | Remapped | NW_003871057.1 |
| NW_004070863.1 | Chr1|NW_004070863.1 | 4 | 20 | Remapped | NW_004070863.1 |
| NW_004070864.2 | Chr1|NW_004070864.2 | 7 | 8 | Remapped | NW_004070864.2 |
| NW_004070865.1 | Chr1|NW_004070865.1 | 2 | 4 | Remapped | NW_004070865.1 |
| NW_003571031.1 | Chr2|NW_003571031.1 | 19 | 27 | Remapped | NW_003571031.1 |
| NW_003571032.1 | Chr2|NW_003571032.1 | 6 | 6 | Remapped | NW_003571032.1 |
| NW_004504299.1 | Chr2|NW_004504299.1 | 22 | 40 | Remapped | NW_004504299.1 |
| NW_003315910.1 | Chr3|NW_003315910.1 | 1 | 1 | Remapped | NW_003315910.1 |
| NW_003315911.1 | Chr3|NW_003315911.1 | 2 | 3 | Remapped | NW_003315911.1 |
| NW_003315912.1 | Chr3|NW_003315912.1 | 3 | 4 | Remapped | NW_003315912.1 |
| NW_003871058.1 | Chr3|NW_003871058.1 | 19 | 36 | Remapped | NW_003871058.1 |
| NW_003871059.1 | Chr3|NW_003871059.1 | 8 | 19 | Remapped | NW_003871059.1 |
| NW_003871060.1 | Chr3|NW_003871060.1 | 10 | 12 | Remapped | NW_003871060.1 |
| NW_004775426.1 | Chr3|NW_004775426.1 | 6 | 14 | Remapped | NW_004775426.1 |
| NT_113885.1 | Chr4|NT_113885.1 | 23 | 77 | Remapped | NT_113885.1 |
| NT_113888.1 | Chr4|NT_113888.1 | 1 | 9 | Remapped | NT_113888.1 |
| NW_003571034.1 | Chr4|NW_003571034.1 | 39 | 99 | Remapped | NW_003571034.1 |
| NW_003571035.1 | Chr4|NW_003571035.1 | 15 | 45 | Remapped | NW_003571035.1 |
| NW_004775427.1 | Chr4|NW_004775427.1 | 22 | 51 | Remapped | NW_004775427.1 |
| NW_003871061.1 | Chr5|NW_003871061.1 | 1 | 1 | Remapped | NW_003871061.1 |
| NW_004775428.1 | Chr5|NW_004775428.1 | 9 | 22 | Remapped | NW_004775428.1 |
| NT_167246.1 | Chr6|NT_167246.1 | 3 | 4 | Remapped | NT_167246.1 |
| NT_167248.1 | Chr6|NT_167248.1 | 3 | 4 | Remapped | NT_167248.1 |
| NT_167249.1 | Chr6|NT_167249.1 | 5 | 6 | Remapped | NT_167249.1 |
| NW_003871062.1 | Chr6|NW_003871062.1 | 13 | 17 | Remapped | NW_003871062.1 |
| NW_004070866.1 | Chr6|NW_004070866.1 | 13 | 36 | Remapped | NW_004070866.1 |
| NW_004166862.1 | Chr6|NW_004166862.1 | 1 | 2 | Remapped | NW_004166862.1 |
| NW_004504300.1 | Chr6|NW_004504300.1 | 32 | 81 | Remapped | NW_004504300.1 |
| NW_004775429.1 | Chr6|NW_004775429.1 | 24 | 51 | Remapped | NW_004775429.1 |
| NT_113901.1 | Chr7|NT_113901.1 | 7 | 13 | Remapped | NT_113901.1 |
| NW_003571037.1 | Chr7|NW_003571037.1 | 14 | 34 | Remapped | NW_003571037.1 |
| NW_003571038.1 | Chr7|NW_003571038.1 | 32 | 73 | Remapped | NW_003571038.1 |
| NW_003571039.1 | Chr7|NW_003571039.1 | 35 | 90 | Remapped | NW_003571039.1 |
| NW_003571040.1 | Chr7|NW_003571040.1 | 23 | 40 | Remapped | NW_003571040.1 |
| NW_003571041.1 | Chr7|NW_003571041.1 | 23 | 49 | Remapped | NW_003571041.1 |
| NW_003871064.1 | Chr7|NW_003871064.1 | 125 | 294 | Remapped | NW_003871064.1 |
| NW_003871065.1 | Chr7|NW_003871065.1 | 10 | 19 | Remapped | NW_003871065.1 |
| NW_004775430.1 | Chr7|NW_004775430.1 | 18 | 31 | Remapped | NW_004775430.1 |
| NW_003315923.1 | Chr8|NW_003315923.1 | 71 | 127 | Remapped | NW_003315923.1 |
| NW_003315924.1 | Chr8|NW_003315924.1 | 51 | 78 | Remapped | NW_003315924.1 |
| NW_003571042.1 | Chr8|NW_003571042.1 | 72 | 112 | Remapped | NW_003571042.1 |
| NW_003871066.2 | Chr8|NW_003871066.2 | 7 | 9 | Remapped | NW_003871066.2 |
| NW_004775431.1 | Chr8|NW_004775431.1 | 1 | 9 | Remapped | NW_004775431.1 |
| NT_113914.1 | Chr9|NT_113914.1 | 6 | 6 | Remapped | NT_113914.1 |
| NT_113916.2 | Chr9|NT_113916.2 | 2 | 9 | Remapped | NT_113916.2 |
| NW_003315925.1 | Chr9|NW_003315925.1 | 32 | 68 | Remapped | NW_003315925.1 |
| NW_003315926.1 | Chr9|NW_003315926.1 | 6 | 16 | Remapped | NW_003315926.1 |
| NW_003315927.1 | Chr9|NW_003315927.1 | 4 | 13 | Remapped | NW_003315927.1 |
| NW_003871067.1 | Chr9|NW_003871067.1 | 7 | 8 | Remapped | NW_003871067.1 |
| NW_004070867.1 | Chr9|NW_004070867.1 | 17 | 26 | Remapped | NW_004070867.1 |
| NW_004070868.1 | Chr9|NW_004070868.1 | 25 | 60 | Remapped | NW_004070868.1 |
| NW_004070869.1 | Chr9|NW_004070869.1 | 8 | 21 | Remapped | NW_004070869.1 |
| NW_004504301.1 | Chr9|NW_004504301.1 | 9 | 19 | Remapped | NW_004504301.1 |
| NW_003315932.1 | Chr10|NW_003315932.1 | 7 | 14 | Remapped | NW_003315932.1 |
| NW_003315933.1 | Chr10|NW_003315933.1 | 10 | 47 | Remapped | NW_003315933.1 |
| NW_003571043.1 | Chr10|NW_003571043.1 | 3 | 4 | Remapped | NW_003571043.1 |
| NW_003871068.1 | Chr10|NW_003871068.1 | 67 | 164 | Remapped | NW_003871068.1 |
| NW_003871069.1 | Chr10|NW_003871069.1 | 4 | 4 | Remapped | NW_003871069.1 |
| NW_003871070.1 | Chr10|NW_003871070.1 | 1 | 1 | Remapped | NW_003871070.1 |
| NW_003871071.1 | Chr10|NW_003871071.1 | 26 | 44 | Remapped | NW_003871071.1 |
| NW_004070870.1 | Chr10|NW_004070870.1 | 29 | 33 | Remapped | NW_004070870.1 |
| NW_004504302.1 | Chr10|NW_004504302.1 | 9 | 15 | Remapped | NW_004504302.1 |
| NW_004775432.1 | Chr10|NW_004775432.1 | 12 | 25 | Remapped | NW_004775432.1 |
| NT_113921.2 | Chr11|NT_113921.2 | 2 | 3 | Remapped | NT_113921.2 |
| NW_003571045.1 | Chr11|NW_003571045.1 | 2 | 2 | Remapped | NW_003571045.1 |
| NW_003571046.1 | Chr11|NW_003571046.1 | 12 | 25 | Remapped | NW_003571046.1 |
| NW_003871072.2 | Chr11|NW_003871072.2 | 13 | 27 | Remapped | NW_003871072.2 |
| NW_003871075.1 | Chr11|NW_003871075.1 | 13 | 31 | Remapped | NW_003871075.1 |
| NW_003871077.1 | Chr11|NW_003871077.1 | 6 | 10 | Remapped | NW_003871077.1 |
| NW_003871078.1 | Chr11|NW_003871078.1 | 2 | 4 | Remapped | NW_003871078.1 |
| NW_003871079.1 | Chr11|NW_003871079.1 | 5 | 28 | Remapped | NW_003871079.1 |
| NW_003871080.1 | Chr11|NW_003871080.1 | 5 | 6 | Remapped | NW_003871080.1 |
| NW_003871081.1 | Chr11|NW_003871081.1 | 13 | 23 | Remapped | NW_003871081.1 |
| NW_004070871.1 | Chr11|NW_004070871.1 | 56 | 97 | Remapped | NW_004070871.1 |
| NW_003315937.1 | Chr12|NW_003315937.1 | 127 | 213 | Remapped | NW_003315937.1 |
| NW_003571048.1 | Chr12|NW_003571048.1 | 38 | 55 | Remapped | NW_003571048.1 |
| NW_003871083.2 | Chr12|NW_003871083.2 | 20 | 48 | Remapped | NW_003871083.2 |
| NW_004504303.2 | Chr12|NW_004504303.2 | 11 | 29 | Remapped | NW_004504303.2 |
| NW_003571051.1 | Chr13|NW_003571051.1 | 3 | 4 | Remapped | NW_003571051.1 |
| NW_004166863.1 | Chr14|NW_004166863.1 | 142 | 275 | Remapped | NW_004166863.1 |
| NW_003871084.1 | Chr15|NW_003871084.1 | 11 | 24 | Remapped | NW_003871084.1 |
| NW_003871085.1 | Chr16|NW_003871085.1 | 2 | 4 | Remapped | NW_003871085.1 |
| NT_113930.1 | Chr17|NT_113930.1 | 3 | 3 | Remapped | NT_113930.1 |
| NW_003315947.1 | Chr17|NW_003315947.1 | 5 | 7 | Remapped | NW_003315947.1 |
| NW_003315948.2 | Chr17|NW_003315948.2 | 6 | 17 | Remapped | NW_003315948.2 |
| NW_003315949.1 | Chr17|NW_003315949.1 | 23 | 45 | Remapped | NW_003315949.1 |
| NW_003315950.2 | Chr17|NW_003315950.2 | 62 | 142 | Remapped | NW_003315950.2 |
| NW_003315951.1 | Chr17|NW_003315951.1 | 17 | 25 | Remapped | NW_003315951.1 |
| NW_003571052.1 | Chr17|NW_003571052.1 | 7 | 7 | Remapped | NW_003571052.1 |
| NW_003871087.1 | Chr17|NW_003871087.1 | 30 | 76 | Remapped | NW_003871087.1 |
| NW_003871088.1 | Chr17|NW_003871088.1 | 25 | 57 | Remapped | NW_003871088.1 |
| NW_003871089.1 | Chr17|NW_003871089.1 | 54 | 100 | Remapped | NW_003871089.1 |
| NW_003871090.1 | Chr17|NW_003871090.1 | 14 | 39 | Remapped | NW_003871090.1 |
| NW_004070872.2 | Chr17|NW_004070872.2 | 228 | 337 | Remapped | NW_004070872.2 |
| NW_004166864.2 | Chr17|NW_004166864.2 | 3 | 4 | Remapped | NW_004166864.2 |
| NW_004775433.1 | Chr17|NW_004775433.1 | 4 | 7 | Remapped | NW_004775433.1 |
| NW_003571053.2 | Chr19|NW_003571053.2 | 27 | 67 | Remapped | NW_003571053.2 |
| NW_003871094.1 | Chr19|NW_003871094.1 | 47 | 86 | Remapped | NW_003871094.1 |
| NW_004166865.1 | Chr19|NW_004166865.1 | 164 | 304 | Remapped | NW_004166865.1 |
| NW_004775434.1 | Chr19|NW_004775434.1 | 17 | 40 | Remapped | NW_004775434.1 |
| NW_003571063.2 | Chr20|NW_003571063.2 | 16 | 49 | Remapped | NW_003571063.2 |
| NW_003871095.1 | Chr20|NW_003871095.1 | 4 | 20 | Remapped | NW_003871095.1 |
| NW_004504304.1 | Chr20|NW_004504304.1 | 22 | 38 | Remapped | NW_004504304.1 |
| NW_003315968.1 | Chr21|NW_003315968.1 | 2 | 6 | Remapped | NW_003315968.1 |
| NW_004775435.1 | Chr21|NW_004775435.1 | 26 | 65 | Remapped | NW_004775435.1 |
| NT_113961.1 | Chr22|NT_113961.1 | 5 | 5 | Remapped | NT_113961.1 |
| NW_003315972.1 | Chr22|NW_003315972.1 | 1 | 1 | Remapped | NW_003315972.1 |
| NW_003871096.1 | Chr22|NW_003871096.1 | 20 | 42 | Remapped | NW_003871096.1 |
| NW_004070874.1 | Chr22|NW_004070874.1 | 10 | 10 | Remapped | NW_004070874.1 |
| NW_004070875.1 | Chr22|NW_004070875.1 | 6 | 12 | Remapped | NW_004070875.1 |
| NW_004070876.1 | Chr22|NW_004070876.1 | 4 | 4 | Remapped | NW_004070876.1 |
| NT_167212.1 | Chr22|NT_167212.1 | 12 | 15 | Remapped | NT_167212.1 |
| NT_167234.1 | Chr22|NT_167234.1 | 4 | 10 | Remapped | NT_167234.1 |
| NT_167235.1 | Chr22|NT_167235.1 | 3 | 19 | Remapped | NT_167235.1 |
| NW_003571064.2 | ChrX|NW_003571064.2 | 60 | 177 | Remapped | NW_003571064.2 |
| NW_003871098.1 | ChrX|NW_003871098.1 | 12 | 20 | Remapped | NW_003871098.1 |
| NW_003871099.1 | ChrX|NW_003871099.1 | 2 | 2 | Remapped | NW_003871099.1 |
| NW_003871100.1 | ChrX|NW_003871100.1 | 31 | 59 | Remapped | NW_003871100.1 |
| NW_003871101.3 | ChrX|NW_003871101.3 | 10 | 22 | Remapped | NW_003871101.3 |
| NW_003871102.1 | ChrX|NW_003871102.1 | 1 | 1 | Remapped | NW_003871102.1 |
| NW_003871103.3 | ChrX|NW_003871103.3 | 109 | 244 | Remapped | NW_003871103.3 |
| NW_004070877.1 | ChrX|NW_004070877.1 | 78 | 186 | Remapped | NW_004070877.1 |
| NW_004070878.1 | ChrX|NW_004070878.1 | 8 | 26 | Remapped | NW_004070878.1 |
| NW_004070879.1 | ChrX|NW_004070879.1 | 14 | 30 | Remapped | NW_004070879.1 |
| NW_004070880.2 | ChrX|NW_004070880.2 | 73 | 160 | Remapped | NW_004070880.2 |
| NW_004070881.1 | ChrX|NW_004070881.1 | 11 | 23 | Remapped | NW_004070881.1 |
| NW_004070882.1 | ChrX|NW_004070882.1 | 8 | 17 | Remapped | NW_004070882.1 |
| NW_004070883.1 | ChrX|NW_004070883.1 | 11 | 24 | Remapped | NW_004070883.1 |
| NW_004070884.1 | ChrX|NW_004070884.1 | 1 | 7 | Remapped | NW_004070884.1 |
| NW_004070885.1 | ChrX|NW_004070885.1 | 20 | 56 | Remapped | NW_004070885.1 |
| NW_004070886.1 | ChrX|NW_004070886.1 | 18 | 24 | Remapped | NW_004070886.1 |
| NW_004070887.1 | ChrX|NW_004070887.1 | 37 | 75 | Remapped | NW_004070887.1 |
| NW_004070888.1 | ChrX|NW_004070888.1 | 39 | 86 | Remapped | NW_004070888.1 |
| NW_004070889.1 | ChrX|NW_004070889.1 | 38 | 80 | Remapped | NW_004070889.1 |
| NW_004070890.2 | ChrX|NW_004070890.2 | 242 | 498 | Remapped | NW_004070890.2 |
| NW_004070891.1 | ChrX|NW_004070891.1 | 55 | 99 | Remapped | NW_004070891.1 |
| NW_004070892.1 | ChrX|NW_004070892.1 | 22 | 43 | Remapped | NW_004070892.1 |
| NW_004070893.1 | ChrX|NW_004070893.1 | 2 | 3 | Remapped | NW_004070893.1 |
| NW_004166866.1 | ChrX|NW_004166866.1 | 18 | 39 | Remapped | NW_004166866.1 |
| Variant Region remap status | Variant Call remap status | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sequence ID | Chr | Variant Regions on source | Perfect | Good | Pass | Fail | Mult | Variant Calls on source | Perfect | Good | Pass | Fail | Mult |
| NC_000001.11 | Chr1 | 7,395 | 7,147 | 30 | 17 | 38 | 163 | 15,661 | 15,090 | 73 | 41 | 102 | 355 |
| NC_000002.12 | Chr2 | 7,206 | 7,003 | 34 | 37 | 85 | 47 | 15,055 | 14,623 | 95 | 94 | 169 | 74 |
| NC_000003.12 | Chr3 | 5,523 | 5,425 | 13 | 11 | 40 | 34 | 11,489 | 11,258 | 37 | 29 | 95 | 70 |
| NC_000004.12 | Chr4 | 6,561 | 6,449 | 23 | 4 | 35 | 50 | 14,022 | 13,727 | 71 | 7 | 98 | 119 |
| NC_000005.10 | Chr5 | 5,800 | 5,773 | 1 | 2 | 14 | 10 | 11,833 | 11,749 | 2 | 11 | 48 | 23 |
| NC_000006.12 | Chr6 | 6,267 | 5,982 | 24 | 22 | 162 | 77 | 13,533 | 12,885 | 86 | 50 | 345 | 167 |
| NC_000007.14 | Chr7 | 6,462 | 6,108 | 42 | 41 | 47 | 224 | 13,313 | 12,471 | 113 | 113 | 97 | 519 |
| NC_000008.11 | Chr8 | 5,175 | 4,998 | 30 | 40 | 28 | 79 | 10,661 | 10,284 | 85 | 95 | 47 | 150 |
| NC_000009.12 | Chr9 | 4,339 | 4,170 | 21 | 29 | 51 | 68 | 9,548 | 9,072 | 76 | 108 | 149 | 143 |
| NC_000010.11 | Chr10 | 4,947 | 4,674 | 14 | 7 | 129 | 123 | 10,068 | 9,466 | 35 | 22 | 288 | 257 |
| NC_000011.10 | Chr11 | 4,829 | 4,653 | 11 | 17 | 42 | 106 | 10,061 | 9,663 | 25 | 60 | 92 | 221 |
| NC_000012.12 | Chr12 | 5,048 | 4,801 | 3 | 5 | 56 | 183 | 10,213 | 9,733 | 15 | 6 | 134 | 325 |
| NC_000013.11 | Chr13 | 3,654 | 3,615 | 7 | 8 | 24 | 0 | 7,797 | 7,681 | 26 | 26 | 64 | 0 |
| NC_000014.9 | Chr14 | 2,746 | 2,624 | 25 | 23 | 14 | 60 | 5,728 | 5,468 | 58 | 53 | 37 | 112 |
| NC_000015.10 | Chr15 | 2,562 | 2,492 | 17 | 12 | 30 | 11 | 5,387 | 5,226 | 43 | 35 | 59 | 24 |
| NC_000016.10 | Chr16 | 3,589 | 3,498 | 14 | 16 | 59 | 2 | 6,788 | 6,567 | 51 | 37 | 129 | 4 |
| NC_000017.11 | Chr17 | 3,894 | 3,597 | 36 | 43 | 94 | 124 | 7,515 | 6,900 | 87 | 80 | 180 | 268 |
| NC_000018.10 | Chr18 | 3,008 | 2,952 | 4 | 5 | 47 | 0 | 5,963 | 5,832 | 9 | 19 | 103 | 0 |
| NC_000019.10 | Chr19 | 3,621 | 3,502 | 18 | 11 | 12 | 78 | 7,020 | 6,746 | 38 | 15 | 45 | 176 |
| NC_000020.11 | Chr20 | 2,809 | 2,648 | 19 | 12 | 93 | 37 | 5,672 | 5,304 | 40 | 53 | 187 | 88 |
| NC_000021.9 | Chr21 | 2,159 | 1,980 | 32 | 20 | 101 | 26 | 4,448 | 4,036 | 116 | 58 | 173 | 65 |
| NC_000022.11 | Chr22 | 2,302 | 2,053 | 71 | 35 | 115 | 28 | 4,637 | 3,953 | 228 | 124 | 281 | 51 |
| NC_000023.11 | ChrX | 4,052 | 3,143 | 27 | 15 | 64 | 803 | 8,454 | 6,477 | 69 | 46 | 153 | 1,709 |
| NC_000024.10 | ChrY | 37 | 35 | 0 | 2 | 0 | 0 | 51 | 46 | 0 | 5 | 0 | 0 |
Samplesets
Number of Samplesets: 1
- Name:
- HGSVG Trios
- Sampleset Type:
- Case
- Description:
- CHS, PUR, and YRI samples represending low diversity, admixture, and high diversity.
- Size:
- 9
- Organisms:
- Homo sapiens
- Sampleset Phenotype(s):
- None reported
| Sample ID | Cell Type | Subject ID | Sex | Ethnicity | Subject Phenotype |
|---|---|---|---|---|---|
| SAMN00006466 | HG00513 | Female | CHS | Not reported | |
| SAMN00001695 | B-Lymphocyte | NA19239 | Male | YRI | Not reported |
| SAMN00001696 | B-Lymphocyte | NA19240 | Female | YRI | Not reported |
| SAMN00001694 | B-Lymphocyte | NA19238 | Female | YRI | Not reported |
| HG00512 | HG00512 | Male | CHS | Not reported | |
| SAMN00006579 | HG00731 | Male | PUR | Not reported | |
| SAMN00006580 | HG00732 | Female | PUR | Not reported | |
| HG00514 | HG00514 | Female | CHS | Not reported | |
| SAMN00006581 | HG00733 | Female | PUR | Not reported |
Experimental Details
| Experiment ID | Type | Method | Analysis | Platforms | Number of Variant Calls |
|---|---|---|---|---|---|
| 1 | Discovery | Optical mapping | Optical mapping | BioNano Genomics | 30,005 |
| 2 | Discovery | Sequencing | Sequence alignment | Illumina HiSeq | 99,464 |
| 3 | Discovery | Sequencing | de novo and local sequence assembly | PacBio RSII | 0 |
| 4 | Discovery | Sequencing | Sequence alignment | Strand-seq | 1,070 |
| 5 | Discovery | Merging of experiments 1,2,3 | Merging of experiments 1,2,3 | See merged experiments | 84,378 |