esv3395724
- Organism: Homo sapiens
- Study:estd59 (1000 Genomes Consortium Pilot Project)
- Variant Type:copy number variation
- Method Type:Sequencing
- Submitted on:NCBI36 (hg18)
- Variant Calls:4
- Validation:Yes
- Clinical Assertions: No
- Region Size:609,911
- Publication(s):1000 Genomes Project Consortium et al. 2010
Source: NCBI
- Genome View
- Variant Region Details and Evidence
- Validation Information
- Clinical Assertions
- Genotype Information
Genome View
Select assembly:Overlapping variant regions from other studies: 1360 SVs from 77 studies. See in: genome view
Overlapping variant regions from other studies: 1880 SVs from 80 studies. See in: genome view
Overlapping variant regions from other studies: 1016 SVs from 64 studies. See in: genome view
Overlapping variant regions from other studies: 1406 SVs from 67 studies. See in: genome view
Overlapping variant regions from other studies: 752 SVs from 54 studies. See in: genome view
Overlapping variant regions from other studies: 1407 SVs from 67 studies. See in: genome view
Overlapping variant regions from other studies: 1856 SVs from 83 studies. See in: genome view
Overlapping variant regions from other studies: 1676 SVs from 53 studies. See in: genome view
Overlapping variant regions from other studies: 1006 SVs from 31 studies. See in: genome view
Variant Region Placement Information
| Variant Region ID | Placement Type | Score | Assembly | Assembly Unit | Reciprocity | Sequence ID | Chr | Start | Stop |
|---|---|---|---|---|---|---|---|---|---|
| esv3395724 | Remapped | Pass | GRCh38.p12 | Primary Assembly | Second Pass | NC_000019.10 | Chr19 | 54,472,537 (-105, +125) | 54,911,985 (-130, +110) |
| esv3395724 | Remapped | Pass | GRCh38.p12 | ALT_REF_LOCI_9 | First Pass | NT_187693.1 | Chr19|NT_1 87693.1 | 454,796 (-105, +125) | 894,467 (-130, +110) |
| esv3395724 | Remapped | Pass | GRCh38.p12 | ALT_REF_LOCI_8 | Second Pass | NW_003571061.2 | Chr19|NW_0 03571061.2 | 363,080 (-105, +125) | 796,479 (-130, +110) |
| esv3395724 | Remapped | Good | GRCh38.p12 | ALT_REF_LOCI_7 | Second Pass | NW_003571060.1 | Chr19|NW_0 03571060.1 | 377,190 (-105, +125) | 987,100 (-130, +110) |
| esv3395724 | Remapped | Pass | GRCh38.p12 | ALT_REF_LOCI_2 | Second Pass | NW_003571055.2 | Chr19|NW_0 03571055.2 | 399,097 (-105, +125) | 729,520 (-130, +110) |
| esv3395724 | Remapped | Good | GRCh38.p12 | ALT_REF_LOCI_1 | Second Pass | NW_003571054.1 | Chr19|NW_0 03571054.1 | 378,949 (-105, +125) | 987,716 (-130, +110) |
| esv3395724 | Remapped | Perfect | GRCh37.p13 | Primary Assembly | First Pass | NC_000019.9 | Chr19 | 54,983,682 (-105, +125) | 55,605,674 (-130, +110) |
| esv3395724 | Remapped | Pass | GRCh37.p13 | PATCHES | First Pass | NW_004166865.1 | Chr19|NW_0 04166865.1 | 667,012 (-105, +125) | 1,058,686 (-130, +110) |
| esv3395724 | Submitted genomic | NCBI36 (hg18) | Primary Assembly | NC_000019.8 | Chr19 | 59,675,494 (-105, +125) | 60,297,486 (-130, +110) |
Variant Call Information
| Variant Call ID | Type | Sample ID | Method | Analysis | Other Calls in this Sample and Study |
|---|---|---|---|---|---|
| essv8749105 | deletion | SAMN00001694 | Sequencing | Paired-end mapping | 29,487 |
| essv8749106 | deletion | SAMN00001695 | Sequencing | Paired-end mapping | 37,049 |
| essv8749108 | deletion | SAMN00001696 | Sequencing | Paired-end mapping | 44,056 |
| essv8749109 | deletion | SAMN00801912 | Sequencing | Paired-end mapping | 25,841 |
Variant Call Placement Information
| Variant Call ID | Placement Type | Score | HGVS | Assembly | Reciprocity | Sequence ID | Chr | Start | Stop |
|---|---|---|---|---|---|---|---|---|---|
| essv8749105 | Remapped | Pass | NT_187693.1:g.(454 691_454921)_(89433 7_894577)del | GRCh38.p12 | First Pass | NT_187693.1 | Chr19|NT_1 87693.1 | 454,796 (-105, +125) | 894,467 (-130, +110) |
| essv8749106 | Remapped | Pass | NT_187693.1:g.(454 691_454921)_(89433 7_894577)del | GRCh38.p12 | First Pass | NT_187693.1 | Chr19|NT_1 87693.1 | 454,796 (-105, +125) | 894,467 (-130, +110) |
| essv8749108 | Remapped | Pass | NT_187693.1:g.(454 691_454921)_(89433 7_894577)del | GRCh38.p12 | First Pass | NT_187693.1 | Chr19|NT_1 87693.1 | 454,796 (-105, +125) | 894,467 (-130, +110) |
| essv8749109 | Remapped | Pass | NT_187693.1:g.(454 691_454921)_(89433 7_894577)del | GRCh38.p12 | First Pass | NT_187693.1 | Chr19|NT_1 87693.1 | 454,796 (-105, +125) | 894,467 (-130, +110) |
| essv8749105 | Remapped | Pass | NW_003571061.2:g.( 362975_363205)_(79 6349_796589)del | GRCh38.p12 | Second Pass | NW_003571061.2 | Chr19|NW_0 03571061.2 | 363,080 (-105, +125) | 796,479 (-130, +110) |
| essv8749106 | Remapped | Pass | NW_003571061.2:g.( 362975_363205)_(79 6349_796589)del | GRCh38.p12 | Second Pass | NW_003571061.2 | Chr19|NW_0 03571061.2 | 363,080 (-105, +125) | 796,479 (-130, +110) |
| essv8749108 | Remapped | Pass | NW_003571061.2:g.( 362975_363205)_(79 6349_796589)del | GRCh38.p12 | Second Pass | NW_003571061.2 | Chr19|NW_0 03571061.2 | 363,080 (-105, +125) | 796,479 (-130, +110) |
| essv8749109 | Remapped | Pass | NW_003571061.2:g.( 362975_363205)_(79 6349_796589)del | GRCh38.p12 | Second Pass | NW_003571061.2 | Chr19|NW_0 03571061.2 | 363,080 (-105, +125) | 796,479 (-130, +110) |
| essv8749105 | Remapped | Good | NW_003571060.1:g.( 377085_377315)_(98 6970_987210)del | GRCh38.p12 | Second Pass | NW_003571060.1 | Chr19|NW_0 03571060.1 | 377,190 (-105, +125) | 987,100 (-130, +110) |
| essv8749106 | Remapped | Good | NW_003571060.1:g.( 377085_377315)_(98 6970_987210)del | GRCh38.p12 | Second Pass | NW_003571060.1 | Chr19|NW_0 03571060.1 | 377,190 (-105, +125) | 987,100 (-130, +110) |
| essv8749108 | Remapped | Good | NW_003571060.1:g.( 377085_377315)_(98 6970_987210)del | GRCh38.p12 | Second Pass | NW_003571060.1 | Chr19|NW_0 03571060.1 | 377,190 (-105, +125) | 987,100 (-130, +110) |
| essv8749109 | Remapped | Good | NW_003571060.1:g.( 377085_377315)_(98 6970_987210)del | GRCh38.p12 | Second Pass | NW_003571060.1 | Chr19|NW_0 03571060.1 | 377,190 (-105, +125) | 987,100 (-130, +110) |
| essv8749105 | Remapped | Pass | NW_003571055.2:g.( 398992_399222)_(72 9390_729630)del | GRCh38.p12 | Second Pass | NW_003571055.2 | Chr19|NW_0 03571055.2 | 399,097 (-105, +125) | 729,520 (-130, +110) |
| essv8749106 | Remapped | Pass | NW_003571055.2:g.( 398992_399222)_(72 9390_729630)del | GRCh38.p12 | Second Pass | NW_003571055.2 | Chr19|NW_0 03571055.2 | 399,097 (-105, +125) | 729,520 (-130, +110) |
| essv8749108 | Remapped | Pass | NW_003571055.2:g.( 398992_399222)_(72 9390_729630)del | GRCh38.p12 | Second Pass | NW_003571055.2 | Chr19|NW_0 03571055.2 | 399,097 (-105, +125) | 729,520 (-130, +110) |
| essv8749109 | Remapped | Pass | NW_003571055.2:g.( 398992_399222)_(72 9390_729630)del | GRCh38.p12 | Second Pass | NW_003571055.2 | Chr19|NW_0 03571055.2 | 399,097 (-105, +125) | 729,520 (-130, +110) |
| essv8749105 | Remapped | Good | NW_003571054.1:g.( 378844_379074)_(98 7586_987826)del | GRCh38.p12 | Second Pass | NW_003571054.1 | Chr19|NW_0 03571054.1 | 378,949 (-105, +125) | 987,716 (-130, +110) |
| essv8749106 | Remapped | Good | NW_003571054.1:g.( 378844_379074)_(98 7586_987826)del | GRCh38.p12 | Second Pass | NW_003571054.1 | Chr19|NW_0 03571054.1 | 378,949 (-105, +125) | 987,716 (-130, +110) |
| essv8749108 | Remapped | Good | NW_003571054.1:g.( 378844_379074)_(98 7586_987826)del | GRCh38.p12 | Second Pass | NW_003571054.1 | Chr19|NW_0 03571054.1 | 378,949 (-105, +125) | 987,716 (-130, +110) |
| essv8749109 | Remapped | Good | NW_003571054.1:g.( 378844_379074)_(98 7586_987826)del | GRCh38.p12 | Second Pass | NW_003571054.1 | Chr19|NW_0 03571054.1 | 378,949 (-105, +125) | 987,716 (-130, +110) |
| essv8749105 | Remapped | Pass | NC_000019.10:g.(54 472432_54472662)_( 54911855_54912095) del | GRCh38.p12 | Second Pass | NC_000019.10 | Chr19 | 54,472,537 (-105, +125) | 54,911,985 (-130, +110) |
| essv8749106 | Remapped | Pass | NC_000019.10:g.(54 472432_54472662)_( 54911855_54912095) del | GRCh38.p12 | Second Pass | NC_000019.10 | Chr19 | 54,472,537 (-105, +125) | 54,911,985 (-130, +110) |
| essv8749108 | Remapped | Pass | NC_000019.10:g.(54 472432_54472662)_( 54911855_54912095) del | GRCh38.p12 | Second Pass | NC_000019.10 | Chr19 | 54,472,537 (-105, +125) | 54,911,985 (-130, +110) |
| essv8749109 | Remapped | Pass | NC_000019.10:g.(54 472432_54472662)_( 54911855_54912095) del | GRCh38.p12 | Second Pass | NC_000019.10 | Chr19 | 54,472,537 (-105, +125) | 54,911,985 (-130, +110) |
| essv8749105 | Remapped | Pass | NW_004166865.1:g.( 666907_667137)_(10 58556_1058796)del | GRCh37.p13 | First Pass | NW_004166865.1 | Chr19|NW_0 04166865.1 | 667,012 (-105, +125) | 1,058,686 (-130, +110) |
| essv8749106 | Remapped | Pass | NW_004166865.1:g.( 666907_667137)_(10 58556_1058796)del | GRCh37.p13 | First Pass | NW_004166865.1 | Chr19|NW_0 04166865.1 | 667,012 (-105, +125) | 1,058,686 (-130, +110) |
| essv8749108 | Remapped | Pass | NW_004166865.1:g.( 666907_667137)_(10 58556_1058796)del | GRCh37.p13 | First Pass | NW_004166865.1 | Chr19|NW_0 04166865.1 | 667,012 (-105, +125) | 1,058,686 (-130, +110) |
| essv8749109 | Remapped | Pass | NW_004166865.1:g.( 666907_667137)_(10 58556_1058796)del | GRCh37.p13 | First Pass | NW_004166865.1 | Chr19|NW_0 04166865.1 | 667,012 (-105, +125) | 1,058,686 (-130, +110) |
| essv8749105 | Remapped | Perfect | NC_000019.9:g.(549 83577_54983807)_(5 5605544_55605784)d el | GRCh37.p13 | First Pass | NC_000019.9 | Chr19 | 54,983,682 (-105, +125) | 55,605,674 (-130, +110) |
| essv8749106 | Remapped | Perfect | NC_000019.9:g.(549 83577_54983807)_(5 5605544_55605784)d el | GRCh37.p13 | First Pass | NC_000019.9 | Chr19 | 54,983,682 (-105, +125) | 55,605,674 (-130, +110) |
| essv8749108 | Remapped | Perfect | NC_000019.9:g.(549 83577_54983807)_(5 5605544_55605784)d el | GRCh37.p13 | First Pass | NC_000019.9 | Chr19 | 54,983,682 (-105, +125) | 55,605,674 (-130, +110) |
| essv8749109 | Remapped | Perfect | NC_000019.9:g.(549 83577_54983807)_(5 5605544_55605784)d el | GRCh37.p13 | First Pass | NC_000019.9 | Chr19 | 54,983,682 (-105, +125) | 55,605,674 (-130, +110) |
| essv8749105 | Submitted genomic | NC_000019.8:g.(596 75389_59675619)_(6 0297356_60297596)d el | NCBI36 (hg18) | NC_000019.8 | Chr19 | 59,675,494 (-105, +125) | 60,297,486 (-130, +110) | ||
| essv8749106 | Submitted genomic | NC_000019.8:g.(596 75389_59675619)_(6 0297356_60297596)d el | NCBI36 (hg18) | NC_000019.8 | Chr19 | 59,675,494 (-105, +125) | 60,297,486 (-130, +110) | ||
| essv8749108 | Submitted genomic | NC_000019.8:g.(596 75389_59675619)_(6 0297356_60297596)d el | NCBI36 (hg18) | NC_000019.8 | Chr19 | 59,675,494 (-105, +125) | 60,297,486 (-130, +110) | ||
| essv8749109 | Submitted genomic | NC_000019.8:g.(596 75389_59675619)_(6 0297356_60297596)d el | NCBI36 (hg18) | NC_000019.8 | Chr19 | 59,675,494 (-105, +125) | 60,297,486 (-130, +110) |
Validation Information
| Variant Call ID | Experiment ID | Sample ID | Method | Analysis | Result |
|---|---|---|---|---|---|
| essv8749105 | 18 | SAMN00001694 | Oligo aCGH | Probe signal intensity | Pass |
| essv8749106 | 18 | SAMN00001695 | Oligo aCGH | Probe signal intensity | Pass |
| essv8749108 | 18 | SAMN00001696 | Oligo aCGH | Probe signal intensity | Pass |
| essv8749109 | 18 | SAMN00801912 | Oligo aCGH | Probe signal intensity | Pass |