nstd207 (Ebert et al. 2021)
- Organism:
- Human
- Study Type:
- Collection
- Submitter:
- Peter A Audano
- Description:
- Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent-child trio data. We present 64 assembled haplotypes from 32 diverse human genomes. These highly contiguous haplotype assemblies (average contig N50: 26 Mbp) integrate all forms of genetic variation even across complex loci. We identify 107,590 structural variants (SVs), of which 68% are not discovered by short-read sequencing, and 278 SV hotspots (spanning megabases of gene-rich sequence). We characterize 130 of the most active mobile element source elements and find that 63% of all SVs arise by homology-mediated mechanisms. This resource enables reliable graph-based genotyping from short reads of up to 50,340 SVs, resulting in the identification of 1,526 expression quantitative trait loci as well as SV candidates for adaptive selection within the human population. See Variant Summary counts for nstd207 in dbVar Variant Summary.
- Publication(s):
- Ebert et al. 2021
Detailed Information: Download 107996 Variant Regions, Download 111746 Variant Calls, Download Both, FTP
Variant Summary
Assembly used for analysis:
Submitted: GRCh38.p9 (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 | 7,194 | 7,455 | Submitted | NC_000001.11 |
| NC_000002.12 | Chr2 | 8,167 | 8,439 | Submitted | NC_000002.12 |
| NC_000003.12 | Chr3 | 5,677 | 5,834 | Submitted | NC_000003.12 |
| NC_000004.12 | Chr4 | 6,464 | 6,688 | Submitted | NC_000004.12 |
| NC_000005.10 | Chr5 | 5,544 | 5,748 | Submitted | NC_000005.10 |
| NC_000006.12 | Chr6 | 5,932 | 6,164 | Submitted | NC_000006.12 |
| NC_000007.14 | Chr7 | 6,765 | 6,997 | Submitted | NC_000007.14 |
| NC_000008.11 | Chr8 | 4,873 | 5,047 | Submitted | NC_000008.11 |
| NC_000009.12 | Chr9 | 4,005 | 4,140 | Submitted | NC_000009.12 |
| NC_000010.11 | Chr10 | 4,938 | 5,132 | Submitted | NC_000010.11 |
| NC_000011.10 | Chr11 | 4,430 | 4,600 | Submitted | NC_000011.10 |
| NC_000012.12 | Chr12 | 4,658 | 4,810 | Submitted | NC_000012.12 |
| NC_000013.11 | Chr13 | 3,673 | 3,794 | Submitted | NC_000013.11 |
| NC_000014.9 | Chr14 | 2,783 | 2,876 | Submitted | NC_000014.9 |
| NC_000015.10 | Chr15 | 2,846 | 2,929 | Submitted | NC_000015.10 |
| NC_000016.10 | Chr16 | 3,955 | 4,101 | Submitted | NC_000016.10 |
| NC_000017.11 | Chr17 | 4,080 | 4,231 | Submitted | NC_000017.11 |
| NC_000018.10 | Chr18 | 2,860 | 2,989 | Submitted | NC_000018.10 |
| NC_000019.10 | Chr19 | 3,604 | 3,732 | Submitted | NC_000019.10 |
| NC_000020.11 | Chr20 | 2,532 | 2,640 | Submitted | NC_000020.11 |
| NC_000021.9 | Chr21 | 1,709 | 1,786 | Submitted | NC_000021.9 |
| NC_000022.11 | Chr22 | 2,256 | 2,354 | Submitted | NC_000022.11 |
| NC_000023.11 | ChrX | 4,215 | 4,336 | Submitted | NC_000023.11 |
| NC_000024.10 | ChrY | 2,189 | 2,250 | Submitted | NC_000024.10 |
| KI270706.1 | Chr1|KI270706.1 | 19 | 19 | Submitted | KI270706.1 |
| KI270712.1 | Chr1|KI270712.1 | 41 | 43 | Submitted | KI270712.1 |
| KI270714.1 | Chr1|KI270714.1 | 1 | 1 | Submitted | KI270714.1 |
| KI270715.1 | Chr2|KI270715.1 | 56 | 56 | Submitted | KI270715.1 |
| KI270716.1 | Chr2|KI270716.1 | 13 | 13 | Submitted | KI270716.1 |
| GL000008.2 | Chr4|GL000008.2 | 38 | 38 | Submitted | GL000008.2 |
| GL000208.1 | Chr19|GL000208.1 | 51 | 51 | Submitted | GL000208.1 |
| KI270719.1 | Chr9|KI270719.1 | 11 | 11 | Submitted | KI270719.1 |
| GL000194.1 | Chr14|GL000194.1 | 34 | 35 | Submitted | GL000194.1 |
| KI270722.1 | Chr14|KI270722.1 | 40 | 40 | Submitted | KI270722.1 |
| KI270723.1 | Chr14|KI270723.1 | 12 | 12 | Submitted | KI270723.1 |
| KI270725.1 | Chr14|KI270725.1 | 21 | 21 | Submitted | KI270725.1 |
| KI270727.1 | Chr15|KI270727.1 | 17 | 17 | Submitted | KI270727.1 |
| KI270728.1 | Chr16|KI270728.1 | 95 | 95 | Submitted | KI270728.1 |
| KI270729.1 | Chr17|KI270729.1 | 87 | 87 | Submitted | KI270729.1 |
| KI270731.1 | Chr22|KI270731.1 | 3 | 3 | Submitted | KI270731.1 |
| KI270732.1 | Chr22|KI270732.1 | 15 | 15 | Submitted | KI270732.1 |
| KI270736.1 | Chr22|KI270736.1 | 67 | 67 | Submitted | KI270736.1 |
| KI270737.1 | Chr22|KI270737.1 | 46 | 46 | Submitted | KI270737.1 |
| KI270738.1 | Chr22|KI270738.1 | 33 | 34 | Submitted | KI270738.1 |
| GL000214.1 | Unplaced|GL000214.1 | 53 | 55 | Submitted | GL000214.1 |
| GL000219.1 | Unplaced|GL000219.1 | 52 | 52 | Submitted | GL000219.1 |
| KI270435.1 | Unplaced|KI270435.1 | 22 | 23 | Submitted | KI270435.1 |
| KI270442.1 | Unplaced|KI270442.1 | 264 | 267 | Submitted | KI270442.1 |
| KI270519.1 | Unplaced|KI270519.1 | 90 | 92 | Submitted | KI270519.1 |
| KI270538.1 | Unplaced|KI270538.1 | 34 | 35 | Submitted | KI270538.1 |
| KI270579.1 | Unplaced|KI270579.1 | 1 | 1 | Submitted | KI270579.1 |
| KI270589.1 | Unplaced|KI270589.1 | 1 | 1 | Submitted | KI270589.1 |
| KI270742.1 | Unplaced|KI270742.1 | 16 | 16 | Submitted | KI270742.1 |
| KI270743.1 | Unplaced|KI270743.1 | 33 | 33 | Submitted | KI270743.1 |
| KI270744.1 | Unplaced|KI270744.1 | 47 | 47 | Submitted | KI270744.1 |
| KI270748.1 | Unplaced|KI270748.1 | 15 | 16 | Submitted | KI270748.1 |
| KI270749.1 | Unplaced|KI270749.1 | 23 | 23 | Submitted | KI270749.1 |
| KI270750.1 | Unplaced|KI270750.1 | 18 | 18 | Submitted | KI270750.1 |
| KI270751.1 | Unplaced|KI270751.1 | 34 | 35 | Submitted | KI270751.1 |
| KI270753.1 | Unplaced|KI270753.1 | 5 | 5 | Submitted | KI270753.1 |
| KI270756.1 | Unplaced|KI270756.1 | 1 | 1 | Submitted | KI270756.1 |
| GL000195.1 | Unplaced|GL000195.1 | 16 | 16 | Submitted | GL000195.1 |
| GL000213.1 | Unplaced|GL000213.1 | 3 | 3 | Submitted | GL000213.1 |
| GL000216.2 | Unplaced|GL000216.2 | 227 | 229 | Submitted | GL000216.2 |
| GL000218.1 | Unplaced|GL000218.1 | 13 | 13 | Submitted | GL000218.1 |
| KI270438.1 | Unplaced|KI270438.1 | 38 | 38 | Submitted | KI270438.1 |
| KI270512.1 | Unplaced|KI270512.1 | 2 | 2 | Submitted | KI270512.1 |
| KI270745.1 | Unplaced|KI270745.1 | 1 | 1 | Submitted | KI270745.1 |
| KI270746.1 | Unplaced|KI270746.1 | 2 | 2 | Submitted | KI270746.1 |
| KI270747.1 | Unplaced|KI270747.1 | 159 | 161 | Submitted | KI270747.1 |
| KI270754.1 | Unplaced|KI270754.1 | 5 | 5 | Submitted | KI270754.1 |
| KI270755.1 | Unplaced|KI270755.1 | 5 | 5 | Submitted | KI270755.1 |
| KI270757.1 | Unplaced|KI270757.1 | 49 | 50 | Submitted | KI270757.1 |
| GL000220.1 | Unplaced|GL000220.1 | 15 | 16 | Submitted | GL000220.1 |
| GL000224.1 | Unplaced|GL000224.1 | 52 | 52 | Submitted | GL000224.1 |
| KI270741.1 | Unplaced|KI270741.1 | 17 | 17 | Submitted | KI270741.1 |
| KI270707.1 | Chr1|KI270707.1 | 6 | 6 | Submitted | KI270707.1 |
| KI270708.1 | Chr1|KI270708.1 | 21 | 21 | Submitted | KI270708.1 |
| KI270709.1 | Chr1|KI270709.1 | 116 | 120 | Submitted | KI270709.1 |
| KI270710.1 | Chr1|KI270710.1 | 1 | 1 | Submitted | KI270710.1 |
| KI270713.1 | Chr1|KI270713.1 | 4 | 4 | Submitted | KI270713.1 |
| GL000221.1 | Chr3|GL000221.1 | 13 | 13 | Submitted | GL000221.1 |
| KI270717.1 | Chr9|KI270717.1 | 3 | 3 | Submitted | KI270717.1 |
| KI270718.1 | Chr9|KI270718.1 | 1 | 1 | Submitted | KI270718.1 |
| KI270720.1 | Chr9|KI270720.1 | 4 | 4 | Submitted | KI270720.1 |
| GL000009.2 | Chr14|GL000009.2 | 29 | 29 | Submitted | GL000009.2 |
| GL000225.1 | Chr14|GL000225.1 | 300 | 300 | Submitted | GL000225.1 |
| KI270724.1 | Chr14|KI270724.1 | 3 | 3 | Submitted | KI270724.1 |
| KI270726.1 | Chr14|KI270726.1 | 3 | 4 | Submitted | KI270726.1 |
| GL000205.2 | Chr17|GL000205.2 | 45 | 45 | Submitted | GL000205.2 |
| KI270730.1 | Chr17|KI270730.1 | 47 | 47 | Submitted | KI270730.1 |
| KI270733.1 | Chr22|KI270733.1 | 12 | 12 | Submitted | KI270733.1 |
| KI270735.1 | Chr22|KI270735.1 | 14 | 14 | Submitted | KI270735.1 |
| KI270739.1 | Chr22|KI270739.1 | 1 | 1 | Submitted | KI270739.1 |
| KI270740.1 | ChrY|KI270740.1 | 11 | 12 | Submitted | KI270740.1 |
| Sequence ID | Chr | Number of Variant Regions | Number of Variant Calls | Placement type | Link to graphical display |
|---|---|---|---|---|---|
| NC_000001.10 | Chr1 | 6,915 | 7,165 | Remapped | NC_000001.10 |
| NC_000002.11 | Chr2 | 8,117 | 8,387 | Remapped | NC_000002.11 |
| NC_000003.11 | Chr3 | 5,638 | 5,790 | Remapped | NC_000003.11 |
| NC_000004.11 | Chr4 | 6,397 | 6,619 | Remapped | NC_000004.11 |
| NC_000005.9 | Chr5 | 5,527 | 5,731 | Remapped | NC_000005.9 |
| NC_000006.11 | Chr6 | 5,754 | 5,979 | Remapped | NC_000006.11 |
| NC_000007.13 | Chr7 | 6,679 | 6,908 | Remapped | NC_000007.13 |
| NC_000008.10 | Chr8 | 4,714 | 4,880 | Remapped | NC_000008.10 |
| NC_000009.11 | Chr9 | 3,925 | 4,058 | Remapped | NC_000009.11 |
| NC_000010.10 | Chr10 | 4,796 | 4,983 | Remapped | NC_000010.10 |
| NC_000011.9 | Chr11 | 4,343 | 4,511 | Remapped | NC_000011.9 |
| NC_000012.11 | Chr12 | 4,596 | 4,747 | Remapped | NC_000012.11 |
| NC_000013.10 | Chr13 | 3,640 | 3,759 | Remapped | NC_000013.10 |
| NC_000014.8 | Chr14 | 2,649 | 2,740 | Remapped | NC_000014.8 |
| NC_000015.9 | Chr15 | 2,838 | 2,921 | Remapped | NC_000015.9 |
| NC_000016.9 | Chr16 | 3,856 | 4,000 | Remapped | NC_000016.9 |
| NC_000017.10 | Chr17 | 3,605 | 3,721 | Remapped | NC_000017.10 |
| NC_000018.9 | Chr18 | 2,839 | 2,967 | Remapped | NC_000018.9 |
| NC_000019.9 | Chr19 | 3,408 | 3,529 | Remapped | NC_000019.9 |
| NC_000020.10 | Chr20 | 2,456 | 2,557 | Remapped | NC_000020.10 |
| NC_000021.8 | Chr21 | 1,706 | 1,783 | Remapped | NC_000021.8 |
| NC_000022.10 | Chr22 | 2,120 | 2,212 | Remapped | NC_000022.10 |
| NC_000023.10 | ChrX | 4,044 | 4,150 | Remapped | NC_000023.10 |
| NC_000024.9 | ChrY | 2,037 | 2,093 | Remapped | NC_000024.9 |
| NT_113923.1 | Unplaced|NT_113923.1 | 9 | 9 | Remapped | NT_113923.1 |
| NT_167222.1 | Unplaced|NT_167222.1 | 3 | 3 | Remapped | NT_167222.1 |
| NT_167207.1 | Chr1|NT_167207.1 | 13 | 13 | Remapped | NT_167207.1 |
| NW_003315903.1 | Chr1|NW_003315903.1 | 19 | 19 | Remapped | NW_003315903.1 |
| NW_003315904.1 | Chr1|NW_003315904.1 | 10 | 10 | Remapped | NW_003315904.1 |
| NW_003571030.1 | Chr1|NW_003571030.1 | 15 | 17 | Remapped | NW_003571030.1 |
| NW_003871055.3 | Chr1|NW_003871055.3 | 345 | 346 | Remapped | NW_003871055.3 |
| NW_003871056.3 | Chr1|NW_003871056.3 | 56 | 56 | Remapped | NW_003871056.3 |
| NW_003871057.1 | Chr1|NW_003871057.1 | 25 | 25 | Remapped | NW_003871057.1 |
| NW_004070863.1 | Chr1|NW_004070863.1 | 2 | 2 | Remapped | NW_004070863.1 |
| NW_004070864.2 | Chr1|NW_004070864.2 | 1 | 1 | Remapped | NW_004070864.2 |
| NW_004070865.1 | Chr1|NW_004070865.1 | 1 | 1 | Remapped | NW_004070865.1 |
| NW_003571031.1 | Chr2|NW_003571031.1 | 18 | 19 | Remapped | NW_003571031.1 |
| NW_003571032.1 | Chr2|NW_003571032.1 | 33 | 33 | Remapped | NW_003571032.1 |
| NW_004504299.1 | Chr2|NW_004504299.1 | 19 | 19 | Remapped | NW_004504299.1 |
| NW_003315910.1 | Chr3|NW_003315910.1 | 2 | 2 | Remapped | NW_003315910.1 |
| NW_003315911.1 | Chr3|NW_003315911.1 | 2 | 3 | Remapped | NW_003315911.1 |
| NW_003315912.1 | Chr3|NW_003315912.1 | 2 | 2 | Remapped | NW_003315912.1 |
| NW_003871058.1 | Chr3|NW_003871058.1 | 20 | 20 | Remapped | NW_003871058.1 |
| NW_003871059.1 | Chr3|NW_003871059.1 | 6 | 6 | Remapped | NW_003871059.1 |
| NW_003871060.1 | Chr3|NW_003871060.1 | 12 | 13 | Remapped | NW_003871060.1 |
| NW_004775426.1 | Chr3|NW_004775426.1 | 2 | 2 | Remapped | NW_004775426.1 |
| NW_003315916.1 | Chr4|NW_003315916.1 | 1 | 1 | Remapped | NW_003315916.1 |
| NW_003571034.1 | Chr4|NW_003571034.1 | 26 | 27 | Remapped | NW_003571034.1 |
| NW_003571035.1 | Chr4|NW_003571035.1 | 18 | 18 | Remapped | NW_003571035.1 |
| NW_004775427.1 | Chr4|NW_004775427.1 | 31 | 32 | Remapped | NW_004775427.1 |
| NW_003871061.1 | Chr5|NW_003871061.1 | 1 | 1 | Remapped | NW_003871061.1 |
| NW_004775428.1 | Chr5|NW_004775428.1 | 3 | 3 | Remapped | NW_004775428.1 |
| NT_167246.1 | Chr6|NT_167246.1 | 2 | 2 | Remapped | NT_167246.1 |
| NT_167248.1 | Chr6|NT_167248.1 | 2 | 2 | Remapped | NT_167248.1 |
| NT_167249.1 | Chr6|NT_167249.1 | 2 | 2 | Remapped | NT_167249.1 |
| NW_003871062.1 | Chr6|NW_003871062.1 | 9 | 9 | Remapped | NW_003871062.1 |
| NW_004070866.1 | Chr6|NW_004070866.1 | 29 | 30 | Remapped | NW_004070866.1 |
| NW_004166862.1 | Chr6|NW_004166862.1 | 2 | 2 | Remapped | NW_004166862.1 |
| NW_004504300.1 | Chr6|NW_004504300.1 | 24 | 24 | Remapped | NW_004504300.1 |
| NW_004775429.1 | Chr6|NW_004775429.1 | 51 | 58 | Remapped | NW_004775429.1 |
| NW_003571037.1 | Chr7|NW_003571037.1 | 22 | 23 | Remapped | NW_003571037.1 |
| NW_003571038.1 | Chr7|NW_003571038.1 | 22 | 22 | Remapped | NW_003571038.1 |
| NW_003571039.1 | Chr7|NW_003571039.1 | 34 | 34 | Remapped | NW_003571039.1 |
| NW_003571040.1 | Chr7|NW_003571040.1 | 48 | 49 | Remapped | NW_003571040.1 |
| NW_003571041.1 | Chr7|NW_003571041.1 | 10 | 11 | Remapped | NW_003571041.1 |
| NW_003871064.1 | Chr7|NW_003871064.1 | 219 | 222 | Remapped | NW_003871064.1 |
| NW_003871065.1 | Chr7|NW_003871065.1 | 10 | 10 | Remapped | NW_003871065.1 |
| NW_004775430.1 | Chr7|NW_004775430.1 | 24 | 24 | Remapped | NW_004775430.1 |
| NW_003315923.1 | Chr8|NW_003315923.1 | 75 | 81 | Remapped | NW_003315923.1 |
| NW_003315924.1 | Chr8|NW_003315924.1 | 37 | 39 | Remapped | NW_003315924.1 |
| NW_003571042.1 | Chr8|NW_003571042.1 | 76 | 77 | Remapped | NW_003571042.1 |
| NW_003871066.2 | Chr8|NW_003871066.2 | 6 | 6 | Remapped | NW_003871066.2 |
| NW_004775431.1 | Chr8|NW_004775431.1 | 5 | 5 | Remapped | NW_004775431.1 |
| NW_003315925.1 | Chr9|NW_003315925.1 | 30 | 30 | Remapped | NW_003315925.1 |
| NW_003315926.1 | Chr9|NW_003315926.1 | 10 | 10 | Remapped | NW_003315926.1 |
| NW_003315927.1 | Chr9|NW_003315927.1 | 7 | 7 | Remapped | NW_003315927.1 |
| NW_003871067.1 | Chr9|NW_003871067.1 | 29 | 29 | Remapped | NW_003871067.1 |
| NW_004070867.1 | Chr9|NW_004070867.1 | 14 | 14 | Remapped | NW_004070867.1 |
| NW_004070868.1 | Chr9|NW_004070868.1 | 18 | 18 | Remapped | NW_004070868.1 |
| NW_004070869.1 | Chr9|NW_004070869.1 | 8 | 11 | Remapped | NW_004070869.1 |
| NW_004504301.1 | Chr9|NW_004504301.1 | 10 | 11 | Remapped | NW_004504301.1 |
| NW_003315932.1 | Chr10|NW_003315932.1 | 9 | 10 | Remapped | NW_003315932.1 |
| NW_003315933.1 | Chr10|NW_003315933.1 | 5 | 6 | Remapped | NW_003315933.1 |
| NW_003571043.1 | Chr10|NW_003571043.1 | 15 | 15 | Remapped | NW_003571043.1 |
| NW_003871068.1 | Chr10|NW_003871068.1 | 122 | 123 | Remapped | NW_003871068.1 |
| NW_003871069.1 | Chr10|NW_003871069.1 | 7 | 7 | Remapped | NW_003871069.1 |
| NW_003871070.1 | Chr10|NW_003871070.1 | 1 | 1 | Remapped | NW_003871070.1 |
| NW_003871071.1 | Chr10|NW_003871071.1 | 37 | 37 | Remapped | NW_003871071.1 |
| NW_004070870.1 | Chr10|NW_004070870.1 | 55 | 61 | Remapped | NW_004070870.1 |
| NW_004504302.1 | Chr10|NW_004504302.1 | 17 | 17 | Remapped | NW_004504302.1 |
| NW_004775432.1 | Chr10|NW_004775432.1 | 10 | 10 | Remapped | NW_004775432.1 |
| NT_113921.2 | Chr11|NT_113921.2 | 2 | 2 | Remapped | NT_113921.2 |
| NW_003571045.1 | Chr11|NW_003571045.1 | 22 | 22 | Remapped | NW_003571045.1 |
| NW_003571046.1 | Chr11|NW_003571046.1 | 21 | 22 | Remapped | NW_003571046.1 |
| NW_003871072.2 | Chr11|NW_003871072.2 | 8 | 9 | Remapped | NW_003871072.2 |
| NW_003871075.1 | Chr11|NW_003871075.1 | 11 | 11 | Remapped | NW_003871075.1 |
| NW_003871076.1 | Chr11|NW_003871076.1 | 2 | 2 | Remapped | NW_003871076.1 |
| NW_003871077.1 | Chr11|NW_003871077.1 | 2 | 2 | Remapped | NW_003871077.1 |
| NW_003871078.1 | Chr11|NW_003871078.1 | 1 | 1 | Remapped | NW_003871078.1 |
| NW_003871079.1 | Chr11|NW_003871079.1 | 6 | 6 | Remapped | NW_003871079.1 |
| NW_003871080.1 | Chr11|NW_003871080.1 | 3 | 3 | Remapped | NW_003871080.1 |
| NW_003871081.1 | Chr11|NW_003871081.1 | 7 | 7 | Remapped | NW_003871081.1 |
| NW_003871082.1 | Chr11|NW_003871082.1 | 1 | 1 | Remapped | NW_003871082.1 |
| NW_004070871.1 | Chr11|NW_004070871.1 | 47 | 47 | Remapped | NW_004070871.1 |
| NW_003315937.1 | Chr12|NW_003315937.1 | 146 | 148 | Remapped | NW_003315937.1 |
| NW_003571048.1 | Chr12|NW_003571048.1 | 38 | 41 | Remapped | NW_003571048.1 |
| NW_003871083.2 | Chr12|NW_003871083.2 | 12 | 12 | Remapped | NW_003871083.2 |
| NW_004504303.2 | Chr12|NW_004504303.2 | 9 | 10 | Remapped | NW_004504303.2 |
| NW_003571051.1 | Chr13|NW_003571051.1 | 3 | 5 | Remapped | NW_003571051.1 |
| NW_004166863.1 | Chr14|NW_004166863.1 | 194 | 197 | Remapped | NW_004166863.1 |
| NW_003871084.1 | Chr15|NW_003871084.1 | 9 | 9 | Remapped | NW_003871084.1 |
| NW_003871085.1 | Chr16|NW_003871085.1 | 1 | 1 | Remapped | NW_003871085.1 |
| NT_113943.1 | Chr17|NT_113943.1 | 2 | 2 | Remapped | NT_113943.1 |
| NW_003315947.1 | Chr17|NW_003315947.1 | 9 | 9 | Remapped | NW_003315947.1 |
| NW_003315948.2 | Chr17|NW_003315948.2 | 6 | 6 | Remapped | NW_003315948.2 |
| NW_003315949.1 | Chr17|NW_003315949.1 | 23 | 23 | Remapped | NW_003315949.1 |
| NW_003315950.2 | Chr17|NW_003315950.2 | 34 | 34 | Remapped | NW_003315950.2 |
| NW_003315951.1 | Chr17|NW_003315951.1 | 18 | 19 | Remapped | NW_003315951.1 |
| NW_003571052.1 | Chr17|NW_003571052.1 | 5 | 5 | Remapped | NW_003571052.1 |
| NW_003871087.1 | Chr17|NW_003871087.1 | 19 | 20 | Remapped | NW_003871087.1 |
| NW_003871088.1 | Chr17|NW_003871088.1 | 27 | 27 | Remapped | NW_003871088.1 |
| NW_003871089.1 | Chr17|NW_003871089.1 | 46 | 48 | Remapped | NW_003871089.1 |
| NW_003871090.1 | Chr17|NW_003871090.1 | 6 | 6 | Remapped | NW_003871090.1 |
| NW_004070872.2 | Chr17|NW_004070872.2 | 381 | 411 | Remapped | NW_004070872.2 |
| NW_004166864.2 | Chr17|NW_004166864.2 | 1 | 1 | Remapped | NW_004166864.2 |
| NW_003571053.2 | Chr19|NW_003571053.2 | 27 | 27 | Remapped | NW_003571053.2 |
| NW_003871094.1 | Chr19|NW_003871094.1 | 36 | 37 | Remapped | NW_003871094.1 |
| NW_004166865.1 | Chr19|NW_004166865.1 | 177 | 184 | Remapped | NW_004166865.1 |
| NW_004775434.1 | Chr19|NW_004775434.1 | 29 | 30 | Remapped | NW_004775434.1 |
| NW_003571063.2 | Chr20|NW_003571063.2 | 26 | 26 | Remapped | NW_003571063.2 |
| NW_003871095.1 | Chr20|NW_003871095.1 | 3 | 3 | Remapped | NW_003871095.1 |
| NW_004504304.1 | Chr20|NW_004504304.1 | 25 | 27 | Remapped | NW_004504304.1 |
| NW_003315968.1 | Chr21|NW_003315968.1 | 1 | 1 | Remapped | NW_003315968.1 |
| NW_004775435.1 | Chr21|NW_004775435.1 | 33 | 33 | Remapped | NW_004775435.1 |
| NT_113961.1 | Chr22|NT_113961.1 | 11 | 11 | Remapped | NT_113961.1 |
| NW_003315972.1 | Chr22|NW_003315972.1 | 1 | 1 | Remapped | NW_003315972.1 |
| NW_003871096.1 | Chr22|NW_003871096.1 | 10 | 10 | Remapped | NW_003871096.1 |
| NW_004070873.1 | Chr22|NW_004070873.1 | 3 | 3 | Remapped | NW_004070873.1 |
| NW_004070874.1 | Chr22|NW_004070874.1 | 31 | 34 | Remapped | NW_004070874.1 |
| NW_004070875.1 | Chr22|NW_004070875.1 | 60 | 60 | Remapped | NW_004070875.1 |
| NW_004070876.1 | Chr22|NW_004070876.1 | 9 | 10 | Remapped | NW_004070876.1 |
| NW_003571064.2 | ChrX|NW_003571064.2 | 107 | 109 | Remapped | NW_003571064.2 |
| NW_003871098.1 | ChrX|NW_003871098.1 | 27 | 27 | Remapped | NW_003871098.1 |
| NW_003871099.1 | ChrX|NW_003871099.1 | 8 | 8 | Remapped | NW_003871099.1 |
| NW_003871100.1 | ChrX|NW_003871100.1 | 18 | 18 | Remapped | NW_003871100.1 |
| NW_003871101.3 | ChrX|NW_003871101.3 | 4 | 4 | Remapped | NW_003871101.3 |
| NW_003871102.1 | ChrX|NW_003871102.1 | 1 | 1 | Remapped | NW_003871102.1 |
| NW_003871103.3 | ChrX|NW_003871103.3 | 107 | 108 | Remapped | NW_003871103.3 |
| NW_004070877.1 | ChrX|NW_004070877.1 | 87 | 90 | Remapped | NW_004070877.1 |
| NW_004070878.1 | ChrX|NW_004070878.1 | 7 | 7 | Remapped | NW_004070878.1 |
| NW_004070879.1 | ChrX|NW_004070879.1 | 8 | 8 | Remapped | NW_004070879.1 |
| NW_004070880.2 | ChrX|NW_004070880.2 | 68 | 69 | Remapped | NW_004070880.2 |
| NW_004070881.1 | ChrX|NW_004070881.1 | 18 | 19 | Remapped | NW_004070881.1 |
| NW_004070882.1 | ChrX|NW_004070882.1 | 11 | 11 | Remapped | NW_004070882.1 |
| NW_004070883.1 | ChrX|NW_004070883.1 | 7 | 7 | Remapped | NW_004070883.1 |
| NW_004070884.1 | ChrX|NW_004070884.1 | 5 | 5 | Remapped | NW_004070884.1 |
| NW_004070885.1 | ChrX|NW_004070885.1 | 9 | 9 | Remapped | NW_004070885.1 |
| NW_004070886.1 | ChrX|NW_004070886.1 | 15 | 15 | Remapped | NW_004070886.1 |
| NW_004070887.1 | ChrX|NW_004070887.1 | 42 | 44 | Remapped | NW_004070887.1 |
| NW_004070888.1 | ChrX|NW_004070888.1 | 41 | 42 | Remapped | NW_004070888.1 |
| NW_004070889.1 | ChrX|NW_004070889.1 | 38 | 41 | Remapped | NW_004070889.1 |
| NW_004070890.2 | ChrX|NW_004070890.2 | 178 | 184 | Remapped | NW_004070890.2 |
| NW_004070891.1 | ChrX|NW_004070891.1 | 45 | 47 | Remapped | NW_004070891.1 |
| NW_004070892.1 | ChrX|NW_004070892.1 | 23 | 23 | Remapped | NW_004070892.1 |
| NW_004070893.1 | ChrX|NW_004070893.1 | 2 | 2 | Remapped | NW_004070893.1 |
| NW_004166866.1 | ChrX|NW_004166866.1 | 9 | 9 | 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 |
| GL000216.2 | Unplaced|GL000216.2 | 227 | 0 | 0 | 0 | 7 | 0 | 229 | 0 | 0 | 0 | 7 | 0 |
| KI270435.1 | Unplaced|KI270435.1 | 22 | 0 | 0 | 0 | 22 | 0 | 23 | 0 | 0 | 0 | 23 | 0 |
| KI270438.1 | Unplaced|KI270438.1 | 38 | 0 | 0 | 0 | 38 | 0 | 38 | 0 | 0 | 0 | 38 | 0 |
| KI270442.1 | Unplaced|KI270442.1 | 264 | 0 | 0 | 0 | 235 | 0 | 267 | 0 | 0 | 0 | 238 | 0 |
| KI270512.1 | Unplaced|KI270512.1 | 2 | 0 | 0 | 0 | 2 | 0 | 2 | 0 | 0 | 0 | 2 | 0 |
| KI270519.1 | Unplaced|KI270519.1 | 90 | 0 | 0 | 0 | 90 | 0 | 92 | 0 | 0 | 0 | 92 | 0 |
| KI270538.1 | Unplaced|KI270538.1 | 34 | 0 | 0 | 0 | 34 | 0 | 35 | 0 | 0 | 0 | 35 | 0 |
| KI270579.1 | Unplaced|KI270579.1 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 0 |
| KI270589.1 | Unplaced|KI270589.1 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 0 |
| KI270708.1 | Chr1|KI270708.1 | 21 | 0 | 0 | 0 | 2 | 0 | 21 | 0 | 0 | 0 | 2 | 0 |
| KI270709.1 | Chr1|KI270709.1 | 116 | 0 | 0 | 0 | 5 | 0 | 120 | 0 | 0 | 0 | 5 | 0 |
| KI270712.1 | Chr1|KI270712.1 | 41 | 0 | 0 | 0 | 21 | 0 | 43 | 0 | 0 | 0 | 23 | 0 |
| KI270715.1 | Chr2|KI270715.1 | 56 | 0 | 0 | 0 | 56 | 0 | 56 | 0 | 0 | 0 | 56 | 0 |
| KI270716.1 | Chr2|KI270716.1 | 13 | 0 | 0 | 0 | 13 | 0 | 13 | 0 | 0 | 0 | 13 | 0 |
| KI270719.1 | Chr9|KI270719.1 | 11 | 0 | 0 | 0 | 2 | 0 | 11 | 0 | 0 | 0 | 2 | 0 |
| KI270720.1 | Chr9|KI270720.1 | 4 | 0 | 0 | 0 | 3 | 0 | 4 | 0 | 0 | 0 | 3 | 0 |
| KI270722.1 | Chr14|KI270722.1 | 40 | 0 | 0 | 0 | 10 | 0 | 40 | 0 | 0 | 0 | 10 | 0 |
| KI270723.1 | Chr14|KI270723.1 | 12 | 0 | 0 | 0 | 10 | 0 | 12 | 0 | 0 | 0 | 10 | 0 |
| KI270724.1 | Chr14|KI270724.1 | 3 | 0 | 0 | 0 | 1 | 0 | 3 | 0 | 0 | 0 | 1 | 0 |
| KI270725.1 | Chr14|KI270725.1 | 21 | 0 | 0 | 0 | 9 | 0 | 21 | 0 | 0 | 0 | 9 | 0 |
| KI270726.1 | Chr14|KI270726.1 | 3 | 0 | 0 | 0 | 2 | 0 | 4 | 0 | 0 | 0 | 3 | 0 |
| KI270727.1 | Chr15|KI270727.1 | 17 | 0 | 0 | 0 | 1 | 0 | 17 | 0 | 0 | 0 | 1 | 0 |
| KI270728.1 | Chr16|KI270728.1 | 95 | 0 | 0 | 0 | 21 | 0 | 95 | 0 | 0 | 0 | 21 | 0 |
| KI270729.1 | Chr17|KI270729.1 | 87 | 0 | 0 | 0 | 38 | 0 | 87 | 0 | 0 | 0 | 38 | 0 |
| KI270730.1 | Chr17|KI270730.1 | 47 | 0 | 0 | 0 | 19 | 0 | 47 | 0 | 0 | 0 | 19 | 0 |
| KI270731.1 | Chr22|KI270731.1 | 3 | 0 | 0 | 0 | 1 | 0 | 3 | 0 | 0 | 0 | 1 | 0 |
| KI270732.1 | Chr22|KI270732.1 | 15 | 0 | 0 | 0 | 9 | 0 | 15 | 0 | 0 | 0 | 9 | 0 |
| KI270733.1 | Chr22|KI270733.1 | 12 | 0 | 0 | 0 | 8 | 0 | 12 | 0 | 0 | 0 | 8 | 0 |
| KI270735.1 | Chr22|KI270735.1 | 14 | 0 | 0 | 0 | 5 | 0 | 14 | 0 | 0 | 0 | 5 | 0 |
| KI270736.1 | Chr22|KI270736.1 | 67 | 0 | 0 | 0 | 67 | 0 | 67 | 0 | 0 | 0 | 67 | 0 |
| KI270737.1 | Chr22|KI270737.1 | 46 | 0 | 0 | 0 | 13 | 0 | 46 | 0 | 0 | 0 | 13 | 0 |
| KI270738.1 | Chr22|KI270738.1 | 33 | 0 | 0 | 0 | 21 | 0 | 34 | 0 | 0 | 0 | 22 | 0 |
| KI270739.1 | Chr22|KI270739.1 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 0 |
| KI270740.1 | ChrY|KI270740.1 | 11 | 0 | 0 | 0 | 11 | 0 | 12 | 0 | 0 | 0 | 12 | 0 |
| KI270741.1 | Unplaced|KI270741.1 | 17 | 0 | 0 | 0 | 4 | 0 | 17 | 0 | 0 | 0 | 4 | 0 |
| KI270743.1 | Unplaced|KI270743.1 | 33 | 0 | 0 | 0 | 3 | 0 | 33 | 0 | 0 | 0 | 3 | 0 |
| KI270744.1 | Unplaced|KI270744.1 | 47 | 0 | 0 | 0 | 6 | 0 | 47 | 0 | 0 | 0 | 6 | 0 |
| KI270747.1 | Unplaced|KI270747.1 | 159 | 0 | 0 | 0 | 146 | 0 | 161 | 0 | 0 | 0 | 148 | 0 |
| KI270748.1 | Unplaced|KI270748.1 | 15 | 0 | 0 | 0 | 7 | 0 | 16 | 0 | 0 | 0 | 8 | 0 |
| KI270749.1 | Unplaced|KI270749.1 | 23 | 0 | 0 | 0 | 8 | 0 | 23 | 0 | 0 | 0 | 8 | 0 |
| KI270750.1 | Unplaced|KI270750.1 | 18 | 0 | 0 | 0 | 6 | 0 | 18 | 0 | 0 | 0 | 6 | 0 |
| KI270751.1 | Unplaced|KI270751.1 | 34 | 0 | 0 | 0 | 16 | 0 | 35 | 0 | 0 | 0 | 17 | 0 |
| KI270753.1 | Unplaced|KI270753.1 | 5 | 0 | 0 | 0 | 5 | 0 | 5 | 0 | 0 | 0 | 5 | 0 |
| KI270755.1 | Unplaced|KI270755.1 | 5 | 0 | 0 | 0 | 3 | 0 | 5 | 0 | 0 | 0 | 3 | 0 |
| KI270756.1 | Unplaced|KI270756.1 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 0 |
| KI270757.1 | Unplaced|KI270757.1 | 49 | 0 | 0 | 0 | 49 | 0 | 50 | 0 | 0 | 0 | 50 | 0 |
| NC_000001.11 | Chr1 | 7,194 | 6,848 | 25 | 10 | 55 | 256 | 7,455 | 7,099 | 25 | 10 | 64 | 257 |
| NC_000002.12 | Chr2 | 8,167 | 8,022 | 21 | 16 | 46 | 62 | 8,439 | 8,291 | 21 | 16 | 48 | 63 |
| NC_000003.12 | Chr3 | 5,677 | 5,593 | 19 | 12 | 23 | 30 | 5,834 | 5,747 | 19 | 12 | 26 | 30 |
| NC_000004.12 | Chr4 | 6,464 | 6,366 | 4 | 0 | 44 | 50 | 6,688 | 6,586 | 4 | 0 | 46 | 52 |
| NC_000005.10 | Chr5 | 5,544 | 5,518 | 1 | 2 | 19 | 4 | 5,748 | 5,722 | 1 | 2 | 19 | 4 |
| NC_000006.12 | Chr6 | 5,932 | 5,624 | 17 | 9 | 170 | 112 | 6,164 | 5,841 | 17 | 9 | 177 | 120 |
| NC_000007.14 | Chr7 | 6,765 | 6,417 | 8 | 6 | 17 | 317 | 6,997 | 6,642 | 8 | 6 | 19 | 322 |
| NC_000008.11 | Chr8 | 4,873 | 4,732 | 13 | 18 | 35 | 75 | 5,047 | 4,897 | 13 | 18 | 39 | 80 |
| NC_000009.12 | Chr9 | 4,005 | 3,852 | 11 | 8 | 39 | 95 | 4,140 | 3,985 | 11 | 8 | 39 | 97 |
| NC_000010.11 | Chr10 | 4,938 | 4,664 | 2 | 3 | 65 | 204 | 5,132 | 4,844 | 2 | 3 | 71 | 212 |
| NC_000011.10 | Chr11 | 4,430 | 4,221 | 2 | 9 | 76 | 122 | 4,600 | 4,387 | 2 | 9 | 78 | 124 |
| NC_000012.12 | Chr12 | 4,658 | 4,497 | 1 | 1 | 8 | 151 | 4,810 | 4,642 | 1 | 1 | 9 | 157 |
| NC_000013.11 | Chr13 | 3,673 | 3,649 | 0 | 1 | 22 | 1 | 3,794 | 3,770 | 0 | 1 | 22 | 1 |
| NC_000014.9 | Chr14 | 2,783 | 2,689 | 10 | 7 | 8 | 69 | 2,876 | 2,779 | 10 | 7 | 9 | 71 |
| NC_000015.10 | Chr15 | 2,846 | 2,810 | 10 | 9 | 8 | 9 | 2,929 | 2,893 | 10 | 9 | 8 | 9 |
| NC_000016.10 | Chr16 | 3,955 | 3,850 | 7 | 12 | 85 | 1 | 4,101 | 3,994 | 7 | 12 | 87 | 1 |
| NC_000017.11 | Chr17 | 4,080 | 3,840 | 17 | 10 | 56 | 157 | 4,231 | 3,986 | 17 | 10 | 59 | 159 |
| NC_000018.10 | Chr18 | 2,860 | 2,836 | 1 | 2 | 21 | 0 | 2,989 | 2,964 | 1 | 2 | 22 | 0 |
| NC_000019.10 | Chr19 | 3,604 | 3,511 | 5 | 3 | 6 | 79 | 3,732 | 3,637 | 5 | 3 | 6 | 81 |
| NC_000020.11 | Chr20 | 2,532 | 2,417 | 2 | 2 | 67 | 44 | 2,640 | 2,516 | 2 | 2 | 74 | 46 |
| NC_000021.9 | Chr21 | 1,709 | 1,670 | 1 | 2 | 3 | 33 | 1,786 | 1,747 | 1 | 2 | 3 | 33 |
| NC_000022.11 | Chr22 | 2,256 | 2,109 | 22 | 19 | 60 | 46 | 2,354 | 2,205 | 22 | 19 | 62 | 46 |
| NC_000023.11 | ChrX | 4,215 | 3,347 | 6 | 4 | 72 | 786 | 4,336 | 3,445 | 6 | 4 | 80 | 801 |
| NC_000024.10 | ChrY | 2,189 | 2,035 | 2 | 0 | 152 | 0 | 2,250 | 2,091 | 2 | 0 | 157 | 0 |
Samplesets
Number of Samplesets: 1
- Sampleset Type:
- Control
- Size:
- 35
- Organisms:
- Homo sapiens
- Sampleset Phenotype(s):
- None reported
| Sample ID | Subject ID | Sex | Ethnicity | Subject Phenotype |
|---|---|---|---|---|
| NA12329 | NA12329 | Female | CEU | Not reported |
| HG02818 | HG02818 | Female | GWD | Not reported |
| HG01114 | HG01114 | Female | CLM | Not reported |
| SAMN00006466 | HG00513 | Female | CHS | Not reported |
| SAMN00000419 | NA18534 | Male | CHB | Not reported |
| SAMN00249812 | HG01596 | Male | KHV | Not reported |
| HG00512 | HG00512 | Male | CHS | Not reported |
| SAMN00006580 | HG00732 | Female | PUR | Not reported |
| SAMN01096687 | HG03009 | Male | BEB | Not reported |
| HG03732 | HG03732 | Male | ITU | Not reported |
| SAMN00249890 | HG00864 | Female | CDX | Not reported |
| SAMN00007824 | NA19983 | Female | ASW | Not reported |
| HG03065 | HG03065 | Male | MSL | Not reported |
| SAMN00001695 | NA19239 | Male | YRI | Not reported |
| HG02587 | HG02587 | Female | GWD | Not reported |
| SAMN00001694 | NA19238 | Female | YRI | Not reported |
| SAMN00004622 | HG00096 | Male | GBR | Not reported |
| HG03371 | HG03371 | Male | ESN | Not reported |
| SAMN00007703 | NA19650 | Male | MXL | Not reported |
| HG02011 | HG02011 | Male | ACB | Not reported |
| SAMN00006581 | HG00733 | Female | PUR | Not reported |
| SAMN00007882 | NA20847 | Female | GIH | Not reported |
| HG03125 | HG03125 | Female | ESN | Not reported |
| NA24385 | NA24385 | Not reported | ||
| SAMN00001229 | NA20509 | Male | TSI | Not reported |
| SAMN00001696 | NA19240 | Female | YRI | Not reported |
| HG03486 | HG03486 | Female | MSL | Not reported |
| HG02492 | HG02492 | Male | PJL | Not reported |
| SAMN00016965 | HG00171 | Female | FIN | Not reported |
| HG03683 | HG03683 | Female | STU | Not reported |
| SAMN00000485 | NA18939 | Female | JPT | Not reported |
| SAMN00801888 | NA12878 | Female | CEU | Not reported |
| SAMN00006579 | HG00731 | Male | PUR | Not reported |
| HG00514 | HG00514 | Female | CHS | Not reported |
| HG01505 | HG01505 | Male | IBS | Not reported |
Experimental Details
| Experiment ID | Type | Method | Analysis | Platforms | Site | Number of Variant Calls |
|---|---|---|---|---|---|---|
| 1 | Discovery | Sequencing | Sequence alignment | PacBio | UW | 0 |
| 2 | Discovery | Sequencing | Sequence alignment | PacBio | UW | 0 |
| 3 | Discovery | Sequencing | Sequence alignment | Illumina | UW | 0 |
| 4 | Discovery | Optical mapping | Optical mapping | Bionano | JAX | 0 |
| 5 | Discovery | Merging of experiments 1,2 | Merging of experiments 1,2 | See merged experiments | UW | 111,330 |
| 6 | Discovery | Merging of experiments 1,2,3,4 | Merging of experiments 1,2,3,4 | See merged experiments | UW | 416 |