esv2669886
- Organism: Homo sapiens
- Study:estd199 (1000 Genomes Consortium Phase 1)
- Variant Type:copy number variation
- Method Type:Sequencing
- Submitted on:GRCh37 (hg19)
- Variant Calls:13
- Validation:Yes
- Clinical Assertions: No
- Region Size:10,448
- Publication(s):1000 Genomes Project Consortium et al. 2012
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: 443 SVs from 77 studies. See in: genome view
Overlapping variant regions from other studies: 442 SVs from 77 studies. See in: genome view
Variant Region Placement Information
| Variant Region ID | Placement Type | Score | Assembly | Assembly Unit | Reciprocity | Sequence ID | Chr | Outer Start | Inner Start | Inner Stop | Outer Stop |
|---|---|---|---|---|---|---|---|---|---|---|---|
| esv2669886 | Remapped | Perfect | GRCh38.p12 | Primary Assembly | First Pass | NC_000003.12 | Chr3 | 52,994,629 | 52,995,000 | 53,004,706 | 53,005,076 |
| esv2669886 | Submitted genomic | GRCh37 (hg19) | Primary Assembly | NC_000003.11 | Chr3 | 53,028,645 | 53,029,016 | 53,038,722 | 53,039,092 |
Variant Call Information
| Variant Call ID | Type | Sample ID | Method | Analysis | Other Calls in this Sample and Study |
|---|---|---|---|---|---|
| essv5405943 | deletion | SAMN00007768 | Sequencing | Paired-end mapping, Read depth, Read depth and paired-end mapping, Split read mapping | 771 |
| essv5604960 | deletion | SAMN00007747 | Sequencing | Paired-end mapping, Read depth, Read depth and paired-end mapping, Split read mapping | 1,108 |
| essv5658411 | deletion | SAMN00007722 | Sequencing | Paired-end mapping, Read depth, Read depth and paired-end mapping, Split read mapping | 1,201 |
| essv5881131 | deletion | SAMN00007798 | Sequencing | Paired-end mapping, Read depth, Read depth and paired-end mapping, Split read mapping | 1,207 |
| essv6133784 | deletion | SAMN00007749 | Sequencing | Paired-end mapping, Read depth, Read depth and paired-end mapping, Split read mapping | 1,120 |
| essv6195578 | deletion | SAMN00007729 | Sequencing | Paired-end mapping, Read depth, Read depth and paired-end mapping, Split read mapping | 1,132 |
| essv6245348 | deletion | SAMN00007767 | Sequencing | Paired-end mapping, Read depth, Read depth and paired-end mapping, Split read mapping | 862 |
| essv6317617 | deletion | SAMN00007732 | Sequencing | Paired-end mapping, Read depth, Read depth and paired-end mapping, Split read mapping | 1,164 |
| essv6335579 | deletion | SAMN00007713 | Sequencing | Paired-end mapping, Read depth, Read depth and paired-end mapping, Split read mapping | 994 |
| essv6369077 | deletion | SAMN00007726 | Sequencing | Paired-end mapping, Read depth, Read depth and paired-end mapping, Split read mapping | 1,102 |
| essv6395895 | deletion | SAMN00007746 | Sequencing | Paired-end mapping, Read depth, Read depth and paired-end mapping, Split read mapping | 1,178 |
| essv6419306 | deletion | SAMN00007776 | Sequencing | Paired-end mapping, Read depth, Read depth and paired-end mapping, Split read mapping | 831 |
| essv6421314 | deletion | SAMN00007755 | Sequencing | Paired-end mapping, Read depth, Read depth and paired-end mapping, Split read mapping | 1,123 |
Variant Call Placement Information
| Variant Call ID | Placement Type | Score | HGVS | Assembly | Reciprocity | Sequence ID | Chr | Outer Start | Inner Start | Inner Stop | Outer Stop |
|---|---|---|---|---|---|---|---|---|---|---|---|
| essv5405943 | Remapped | Perfect | NC_000003.12:g.(52 994629_52995000)_( 53004706_53005076) del | GRCh38.p12 | First Pass | NC_000003.12 | Chr3 | 52,994,629 | 52,995,000 | 53,004,706 | 53,005,076 |
| essv5604960 | Remapped | Perfect | NC_000003.12:g.(52 994629_52995000)_( 53004706_53005076) del | GRCh38.p12 | First Pass | NC_000003.12 | Chr3 | 52,994,629 | 52,995,000 | 53,004,706 | 53,005,076 |
| essv5658411 | Remapped | Perfect | NC_000003.12:g.(52 994629_52995000)_( 53004706_53005076) del | GRCh38.p12 | First Pass | NC_000003.12 | Chr3 | 52,994,629 | 52,995,000 | 53,004,706 | 53,005,076 |
| essv5881131 | Remapped | Perfect | NC_000003.12:g.(52 994629_52995000)_( 53004706_53005076) del | GRCh38.p12 | First Pass | NC_000003.12 | Chr3 | 52,994,629 | 52,995,000 | 53,004,706 | 53,005,076 |
| essv6133784 | Remapped | Perfect | NC_000003.12:g.(52 994629_52995000)_( 53004706_53005076) del | GRCh38.p12 | First Pass | NC_000003.12 | Chr3 | 52,994,629 | 52,995,000 | 53,004,706 | 53,005,076 |
| essv6195578 | Remapped | Perfect | NC_000003.12:g.(52 994629_52995000)_( 53004706_53005076) del | GRCh38.p12 | First Pass | NC_000003.12 | Chr3 | 52,994,629 | 52,995,000 | 53,004,706 | 53,005,076 |
| essv6245348 | Remapped | Perfect | NC_000003.12:g.(52 994629_52995000)_( 53004706_53005076) del | GRCh38.p12 | First Pass | NC_000003.12 | Chr3 | 52,994,629 | 52,995,000 | 53,004,706 | 53,005,076 |
| essv6317617 | Remapped | Perfect | NC_000003.12:g.(52 994629_52995000)_( 53004706_53005076) del | GRCh38.p12 | First Pass | NC_000003.12 | Chr3 | 52,994,629 | 52,995,000 | 53,004,706 | 53,005,076 |
| essv6335579 | Remapped | Perfect | NC_000003.12:g.(52 994629_52995000)_( 53004706_53005076) del | GRCh38.p12 | First Pass | NC_000003.12 | Chr3 | 52,994,629 | 52,995,000 | 53,004,706 | 53,005,076 |
| essv6369077 | Remapped | Perfect | NC_000003.12:g.(52 994629_52995000)_( 53004706_53005076) del | GRCh38.p12 | First Pass | NC_000003.12 | Chr3 | 52,994,629 | 52,995,000 | 53,004,706 | 53,005,076 |
| essv6395895 | Remapped | Perfect | NC_000003.12:g.(52 994629_52995000)_( 53004706_53005076) del | GRCh38.p12 | First Pass | NC_000003.12 | Chr3 | 52,994,629 | 52,995,000 | 53,004,706 | 53,005,076 |
| essv6419306 | Remapped | Perfect | NC_000003.12:g.(52 994629_52995000)_( 53004706_53005076) del | GRCh38.p12 | First Pass | NC_000003.12 | Chr3 | 52,994,629 | 52,995,000 | 53,004,706 | 53,005,076 |
| essv6421314 | Remapped | Perfect | NC_000003.12:g.(52 994629_52995000)_( 53004706_53005076) del | GRCh38.p12 | First Pass | NC_000003.12 | Chr3 | 52,994,629 | 52,995,000 | 53,004,706 | 53,005,076 |
| essv5405943 | Submitted genomic | NC_000003.11:g.(53 028645_53029016)_( 53038722_53039092) del | GRCh37 (hg19) | NC_000003.11 | Chr3 | 53,028,645 | 53,029,016 | 53,038,722 | 53,039,092 | ||
| essv5604960 | Submitted genomic | NC_000003.11:g.(53 028645_53029016)_( 53038722_53039092) del | GRCh37 (hg19) | NC_000003.11 | Chr3 | 53,028,645 | 53,029,016 | 53,038,722 | 53,039,092 | ||
| essv5658411 | Submitted genomic | NC_000003.11:g.(53 028645_53029016)_( 53038722_53039092) del | GRCh37 (hg19) | NC_000003.11 | Chr3 | 53,028,645 | 53,029,016 | 53,038,722 | 53,039,092 | ||
| essv5881131 | Submitted genomic | NC_000003.11:g.(53 028645_53029016)_( 53038722_53039092) del | GRCh37 (hg19) | NC_000003.11 | Chr3 | 53,028,645 | 53,029,016 | 53,038,722 | 53,039,092 | ||
| essv6133784 | Submitted genomic | NC_000003.11:g.(53 028645_53029016)_( 53038722_53039092) del | GRCh37 (hg19) | NC_000003.11 | Chr3 | 53,028,645 | 53,029,016 | 53,038,722 | 53,039,092 | ||
| essv6195578 | Submitted genomic | NC_000003.11:g.(53 028645_53029016)_( 53038722_53039092) del | GRCh37 (hg19) | NC_000003.11 | Chr3 | 53,028,645 | 53,029,016 | 53,038,722 | 53,039,092 | ||
| essv6245348 | Submitted genomic | NC_000003.11:g.(53 028645_53029016)_( 53038722_53039092) del | GRCh37 (hg19) | NC_000003.11 | Chr3 | 53,028,645 | 53,029,016 | 53,038,722 | 53,039,092 | ||
| essv6317617 | Submitted genomic | NC_000003.11:g.(53 028645_53029016)_( 53038722_53039092) del | GRCh37 (hg19) | NC_000003.11 | Chr3 | 53,028,645 | 53,029,016 | 53,038,722 | 53,039,092 | ||
| essv6335579 | Submitted genomic | NC_000003.11:g.(53 028645_53029016)_( 53038722_53039092) del | GRCh37 (hg19) | NC_000003.11 | Chr3 | 53,028,645 | 53,029,016 | 53,038,722 | 53,039,092 | ||
| essv6369077 | Submitted genomic | NC_000003.11:g.(53 028645_53029016)_( 53038722_53039092) del | GRCh37 (hg19) | NC_000003.11 | Chr3 | 53,028,645 | 53,029,016 | 53,038,722 | 53,039,092 | ||
| essv6395895 | Submitted genomic | NC_000003.11:g.(53 028645_53029016)_( 53038722_53039092) del | GRCh37 (hg19) | NC_000003.11 | Chr3 | 53,028,645 | 53,029,016 | 53,038,722 | 53,039,092 | ||
| essv6419306 | Submitted genomic | NC_000003.11:g.(53 028645_53029016)_( 53038722_53039092) del | GRCh37 (hg19) | NC_000003.11 | Chr3 | 53,028,645 | 53,029,016 | 53,038,722 | 53,039,092 | ||
| essv6421314 | Submitted genomic | NC_000003.11:g.(53 028645_53029016)_( 53038722_53039092) del | GRCh37 (hg19) | NC_000003.11 | Chr3 | 53,028,645 | 53,029,016 | 53,038,722 | 53,039,092 |
Validation Information
| Variant Call ID | Experiment ID | Sample ID | Method | Analysis | Result |
|---|---|---|---|---|---|
| essv6335579 | 7 | SAMN00007713 | SNP array | Probe signal intensity | Pass |
| essv5658411 | 7 | SAMN00007722 | SNP array | Probe signal intensity | Pass |
| essv6369077 | 7 | SAMN00007726 | SNP array | Probe signal intensity | Pass |
| essv6195578 | 7 | SAMN00007729 | SNP array | Probe signal intensity | Pass |
| essv6317617 | 7 | SAMN00007732 | SNP array | Probe signal intensity | Pass |
| essv6395895 | 7 | SAMN00007746 | SNP array | Probe signal intensity | Pass |
| essv5604960 | 7 | SAMN00007747 | SNP array | Probe signal intensity | Pass |
| essv6133784 | 7 | SAMN00007749 | SNP array | Probe signal intensity | Pass |
| essv6421314 | 7 | SAMN00007755 | SNP array | Probe signal intensity | Pass |
| essv6245348 | 7 | SAMN00007767 | SNP array | Probe signal intensity | Pass |
| essv5405943 | 7 | SAMN00007768 | SNP array | Probe signal intensity | Pass |
| essv6419306 | 7 | SAMN00007776 | SNP array | Probe signal intensity | Pass |
| essv5881131 | 7 | SAMN00007798 | SNP array | Probe signal intensity | Pass |