nstd46 (Campbell et al. 2011)
- Organism:
- Human
- Study Type:
- Control Set
- Submitter:
- Katie Campbell
- Description:
- Copy number variants (CNVs) can reach appreciable frequencies in the human population, and several of these copy number polymorphisms (CNPs) have been recently associated with human diseases including lupus, psoriasis, Crohn disease, and obesity. Despite new advances, significant biases remain in terms of CNP discovery and genotyping. We developed a novel method based on single channel intensity data and benchmarked against copy numbers determined from sequencing read-depth to successfully obtain CNP genotypes for 1489 CNPs from 487 human DNA samples from diverse ethnic backgrounds. This customized microarray was enriched for segmental duplication-rich regions and novel insertions of sequences not represented in the reference genome assembly or on standard single nucleotide polymorphism (SNP) microarray platforms. We observe that CNPs in segmental duplications are more likely to be population differentiated than CNPs in unique regions (p = 0.015) and that bi-allelic CNPs show greater stratification when compared to frequency-matched SNPs (p = 0.0026). Although bi-allelic CNPs show a strong correlation of copy number with flanking SNP genotypes, the majority of multi-copy CNPs do not (40% with r >0.8). We selected a subset of CNPs for further characterization in 1873 additional samples from 62 populations; this revealed striking population-differentiated structural variants in genes of clinical significance such as the OCLN gene, a tight junction protein involved in hepatitis C viral entry. Our new microarray design allows these variants to be rapidly tested for disease association and our results suggest that CNPs (especially those not in linkage disequilibrium with SNPs) may have contributed disproportionately to human diversity and selection. See Variant Summary counts for nstd46 in dbVar Variant Summary.
- Publication(s):
- Campbell et al. 2011
Detailed Information: Download 1183 Variant Regions, Download 227380 Variant Calls, Download Both, FTP
Variant Summary
Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Remapped: GRCh37.p13 (hg19)
Submitted: NCBI36 (hg18)
| Sequence ID | Chr | Number of Variant Regions | Number of Variant Calls | Placement type | Link to graphical display |
|---|---|---|---|---|---|
| NC_000001.11 | Chr1 | 86 | 17,390 | Remapped | NC_000001.11 |
| NC_000002.12 | Chr2 | 94 | 16,475 | Remapped | NC_000002.12 |
| NC_000003.12 | Chr3 | 76 | 12,328 | Remapped | NC_000003.12 |
| NC_000004.12 | Chr4 | 100 | 14,200 | Remapped | NC_000004.12 |
| NC_000005.10 | Chr5 | 62 | 10,988 | Remapped | NC_000005.10 |
| NC_000006.12 | Chr6 | 74 | 13,196 | Remapped | NC_000006.12 |
| NC_000007.14 | Chr7 | 68 | 12,288 | Remapped | NC_000007.14 |
| NC_000008.11 | Chr8 | 92 | 17,874 | Remapped | NC_000008.11 |
| NC_000009.12 | Chr9 | 43 | 7,375 | Remapped | NC_000009.12 |
| NC_000010.11 | Chr10 | 50 | 10,071 | Remapped | NC_000010.11 |
| NC_000011.10 | Chr11 | 53 | 8,262 | Remapped | NC_000011.10 |
| NC_000012.12 | Chr12 | 45 | 7,343 | Remapped | NC_000012.12 |
| NC_000013.11 | Chr13 | 30 | 5,332 | Remapped | NC_000013.11 |
| NC_000014.9 | Chr14 | 42 | 10,700 | Remapped | NC_000014.9 |
| NC_000015.10 | Chr15 | 32 | 6,922 | Remapped | NC_000015.10 |
| NC_000016.10 | Chr16 | 32 | 7,668 | Remapped | NC_000016.10 |
| NC_000017.11 | Chr17 | 35 | 9,363 | Remapped | NC_000017.11 |
| NC_000018.10 | Chr18 | 27 | 4,068 | Remapped | NC_000018.10 |
| NC_000019.10 | Chr19 | 19 | 4,882 | Remapped | NC_000019.10 |
| NC_000020.11 | Chr20 | 18 | 3,344 | Remapped | NC_000020.11 |
| NC_000021.9 | Chr21 | 10 | 938 | Remapped | NC_000021.9 |
| NC_000022.11 | Chr22 | 14 | 4,328 | Remapped | NC_000022.11 |
| NC_000023.11 | ChrX | 64 | 18,539 | Remapped | NC_000023.11 |
| NC_000024.10 | ChrY | 8 | 570 | Remapped | NC_000024.10 |
| NT_187518.1 | Chr1|NT_187518.1 | 1 | 167 | Remapped | NT_187518.1 |
| NT_187646.1 | Chr1|NT_187646.1 | 1 | 167 | Remapped | NT_187646.1 |
| NW_011332687.1 | Chr1|NW_011332687.1 | 1 | 11 | Remapped | NW_011332687.1 |
| NW_017852928.1 | Chr1|NW_017852928.1 | 2 | 562 | Remapped | NW_017852928.1 |
| NW_018654707.1 | Chr1|NW_018654707.1 | 2 | 520 | Remapped | NW_018654707.1 |
| NT_187523.1 | Chr2|NT_187523.1 | 2 | 496 | Remapped | NT_187523.1 |
| NT_187528.1 | Chr2|NT_187528.1 | 1 | 488 | Remapped | NT_187528.1 |
| NT_187529.1 | Chr2|NT_187529.1 | 1 | 488 | Remapped | NT_187529.1 |
| NT_187530.1 | Chr2|NT_187530.1 | 1 | 6 | Remapped | NT_187530.1 |
| NT_187647.1 | Chr2|NT_187647.1 | 2 | 496 | Remapped | NT_187647.1 |
| NW_012132915.1 | Chr2|NW_012132915.1 | 1 | 244 | Remapped | NW_012132915.1 |
| NT_187678.1 | Chr3|NT_187678.1 | 2 | 966 | Remapped | NT_187678.1 |
| NT_187688.1 | Chr3|NT_187688.1 | 1 | 478 | Remapped | NT_187688.1 |
| NT_187689.1 | Chr3|NT_187689.1 | 1 | 478 | Remapped | NT_187689.1 |
| NT_187690.1 | Chr3|NT_187690.1 | 1 | 478 | Remapped | NT_187690.1 |
| NT_187691.1 | Chr3|NT_187691.1 | 1 | 478 | Remapped | NT_187691.1 |
| NT_187532.1 | Chr3|NT_187532.1 | 1 | 478 | Remapped | NT_187532.1 |
| NT_187536.1 | Chr3|NT_187536.1 | 1 | 36 | Remapped | NT_187536.1 |
| NT_187649.1 | Chr3|NT_187649.1 | 1 | 478 | Remapped | NT_187649.1 |
| NT_187545.1 | Chr4|NT_187545.1 | 1 | 488 | Remapped | NT_187545.1 |
| NW_003315915.1 | Chr4|NW_003315915.1 | 1 | 159 | Remapped | NW_003315915.1 |
| NT_187651.1 | Chr5|NT_187651.1 | 2 | 821 | Remapped | NT_187651.1 |
| NT_167246.2 | Chr6|NT_167246.2 | 4 | 1,120 | Remapped | NT_167246.2 |
| NT_167247.2 | Chr6|NT_167247.2 | 2 | 840 | Remapped | NT_167247.2 |
| NT_167249.2 | Chr6|NT_167249.2 | 7 | 2,415 | Remapped | NT_167249.2 |
| NT_167245.2 | Chr6|NT_167245.2 | 3 | 1,311 | Remapped | NT_167245.2 |
| NT_187558.1 | Chr7|NT_187558.1 | 1 | 54 | Remapped | NT_187558.1 |
| NT_187560.1 | Chr7|NT_187560.1 | 1 | 488 | Remapped | NT_187560.1 |
| NT_187562.1 | Chr7|NT_187562.1 | 3 | 968 | Remapped | NT_187562.1 |
| NT_187653.1 | Chr7|NT_187653.1 | 1 | 54 | Remapped | NT_187653.1 |
| NW_018654714.1 | Chr7|NW_018654714.1 | 1 | 207 | Remapped | NW_018654714.1 |
| NW_018654715.1 | Chr7|NW_018654715.1 | 2 | 976 | Remapped | NW_018654715.1 |
| NT_187570.1 | Chr8|NT_187570.1 | 3 | 1,375 | Remapped | NT_187570.1 |
| NT_187576.1 | Chr8|NT_187576.1 | 4 | 672 | Remapped | NT_187576.1 |
| NW_018654717.1 | Chr8|NW_018654717.1 | 9 | 3,684 | Remapped | NW_018654717.1 |
| NW_003315931.1 | Chr9|NW_003315931.1 | 1 | 488 | Remapped | NW_003315931.1 |
| NW_003315934.1 | Chr10|NW_003315934.1 | 1 | 112 | Remapped | NW_003315934.1 |
| NW_013171806.1 | Chr10|NW_013171806.1 | 2 | 223 | Remapped | NW_013171806.1 |
| NT_187581.1 | Chr11|NT_187581.1 | 1 | 488 | Remapped | NT_187581.1 |
| NT_187583.1 | Chr11|NT_187583.1 | 1 | 119 | Remapped | NT_187583.1 |
| NW_011332695.1 | Chr11|NW_011332695.1 | 1 | 119 | Remapped | NW_011332695.1 |
| NW_019805495.1 | Chr11|NW_019805495.1 | 1 | 46 | Remapped | NW_019805495.1 |
| NT_187658.1 | Chr12|NT_187658.1 | 2 | 487 | Remapped | NT_187658.1 |
| NT_187587.1 | Chr12|NT_187587.1 | 2 | 524 | Remapped | NT_187587.1 |
| NW_003315940.1 | Chr12|NW_003315940.1 | 1 | 486 | Remapped | NW_003315940.1 |
| NW_003571050.1 | Chr12|NW_003571050.1 | 1 | 66 | Remapped | NW_003571050.1 |
| NW_011332696.1 | Chr12|NW_011332696.1 | 1 | 26 | Remapped | NW_011332696.1 |
| NW_018654718.1 | Chr12|NW_018654718.1 | 1 | 23 | Remapped | NW_018654718.1 |
| NW_019805499.1 | Chr12|NW_019805499.1 | 1 | 12 | Remapped | NW_019805499.1 |
| NT_187600.1 | Chr14|NT_187600.1 | 4 | 917 | Remapped | NT_187600.1 |
| NT_187660.1 | Chr15|NT_187660.1 | 1 | 74 | Remapped | NT_187660.1 |
| NW_011332701.1 | Chr15|NW_011332701.1 | 1 | 74 | Remapped | NW_011332701.1 |
| NT_187607.1 | Chr16|NT_187607.1 | 1 | 13 | Remapped | NT_187607.1 |
| NT_187661.1 | Chr17|NT_187661.1 | 4 | 1,603 | Remapped | NT_187661.1 |
| NT_187663.1 | Chr17|NT_187663.1 | 1 | 118 | Remapped | NT_187663.1 |
| NW_003871093.1 | Chr17|NW_003871093.1 | 1 | 400 | Remapped | NW_003871093.1 |
| NT_187614.1 | Chr17|NT_187614.1 | 4 | 1,304 | Remapped | NT_187614.1 |
| NW_003315953.2 | Chr17|NW_003315953.2 | 1 | 53 | Remapped | NW_003315953.2 |
| NW_003871092.1 | Chr17|NW_003871092.1 | 1 | 109 | Remapped | NW_003871092.1 |
| NW_017363819.1 | Chr17|NW_017363819.1 | 1 | 377 | Remapped | NW_017363819.1 |
| NT_187666.1 | Chr18|NT_187666.1 | 1 | 488 | Remapped | NT_187666.1 |
| NW_003315961.1 | Chr18|NW_003315961.1 | 1 | 488 | Remapped | NW_003315961.1 |
| NT_187693.1 | Chr19|NT_187693.1 | 2 | 732 | Remapped | NT_187693.1 |
| NW_003571060.1 | Chr19|NW_003571060.1 | 1 | 244 | Remapped | NW_003571060.1 |
| NW_003571054.1 | Chr19|NW_003571054.1 | 1 | 244 | Remapped | NW_003571054.1 |
| NT_187623.1 | Chr20|NT_187623.1 | 1 | 488 | Remapped | NT_187623.1 |
| NT_187624.1 | Chr20|NT_187624.1 | 1 | 488 | Remapped | NT_187624.1 |
| NW_003315968.2 | Chr21|NW_003315968.2 | 1 | 68 | Remapped | NW_003315968.2 |
| NT_187629.1 | Chr22|NT_187629.1 | 1 | 436 | Remapped | NT_187629.1 |
| NT_187632.1 | Chr22|NT_187632.1 | 1 | 488 | Remapped | NT_187632.1 |
| NT_187633.1 | Chr22|NT_187633.1 | 1 | 272 | Remapped | NT_187633.1 |
| NW_003315972.2 | Chr22|NW_003315972.2 | 1 | 140 | Remapped | NW_003315972.2 |
| Sequence ID | Chr | Number of Variant Regions | Number of Variant Calls | Placement type | Link to graphical display |
|---|---|---|---|---|---|
| NC_000001.10 | Chr1 | 85 | 16,902 | Remapped | NC_000001.10 |
| NC_000002.11 | Chr2 | 95 | 16,796 | Remapped | NC_000002.11 |
| NC_000003.11 | Chr3 | 76 | 12,328 | Remapped | NC_000003.11 |
| NC_000004.11 | Chr4 | 100 | 14,200 | Remapped | NC_000004.11 |
| NC_000005.9 | Chr5 | 62 | 10,988 | Remapped | NC_000005.9 |
| NC_000006.11 | Chr6 | 74 | 13,196 | Remapped | NC_000006.11 |
| NC_000007.13 | Chr7 | 68 | 12,288 | Remapped | NC_000007.13 |
| NC_000008.10 | Chr8 | 93 | 18,036 | Remapped | NC_000008.10 |
| NC_000009.11 | Chr9 | 43 | 7,375 | Remapped | NC_000009.11 |
| NC_000010.10 | Chr10 | 50 | 10,071 | Remapped | NC_000010.10 |
| NC_000011.9 | Chr11 | 53 | 8,262 | Remapped | NC_000011.9 |
| NC_000012.11 | Chr12 | 45 | 7,343 | Remapped | NC_000012.11 |
| NC_000013.10 | Chr13 | 30 | 5,332 | Remapped | NC_000013.10 |
| NC_000014.8 | Chr14 | 43 | 10,919 | Remapped | NC_000014.8 |
| NC_000015.9 | Chr15 | 32 | 6,922 | Remapped | NC_000015.9 |
| NC_000016.9 | Chr16 | 32 | 7,668 | Remapped | NC_000016.9 |
| NC_000017.10 | Chr17 | 36 | 9,470 | Remapped | NC_000017.10 |
| NC_000018.9 | Chr18 | 28 | 4,556 | Remapped | NC_000018.9 |
| NC_000019.9 | Chr19 | 19 | 4,882 | Remapped | NC_000019.9 |
| NC_000020.10 | Chr20 | 18 | 3,344 | Remapped | NC_000020.10 |
| NC_000021.8 | Chr21 | 10 | 938 | Remapped | NC_000021.8 |
| NC_000022.10 | Chr22 | 15 | 4,600 | Remapped | NC_000022.10 |
| NC_000023.10 | ChrX | 64 | 18,539 | Remapped | NC_000023.10 |
| NC_000024.9 | ChrY | 8 | 570 | Remapped | NC_000024.9 |
| NW_003315903.1 | Chr1|NW_003315903.1 | 1 | 111 | Remapped | NW_003315903.1 |
| NW_003871056.3 | Chr1|NW_003871056.3 | 1 | 488 | Remapped | NW_003871056.3 |
| NW_003315915.1 | Chr4|NW_003315915.1 | 1 | 159 | Remapped | NW_003315915.1 |
| NW_004775427.1 | Chr4|NW_004775427.1 | 1 | 488 | Remapped | NW_004775427.1 |
| NW_004775428.1 | Chr5|NW_004775428.1 | 1 | 80 | Remapped | NW_004775428.1 |
| NT_167245.1 | Chr6|NT_167245.1 | 3 | 1,311 | Remapped | NT_167245.1 |
| NT_167246.1 | Chr6|NT_167246.1 | 4 | 1,120 | Remapped | NT_167246.1 |
| NT_167247.1 | Chr6|NT_167247.1 | 2 | 840 | Remapped | NT_167247.1 |
| NT_167249.1 | Chr6|NT_167249.1 | 7 | 2,415 | Remapped | NT_167249.1 |
| NW_004070866.1 | Chr6|NW_004070866.1 | 1 | 488 | Remapped | NW_004070866.1 |
| NW_003571040.1 | Chr7|NW_003571040.1 | 3 | 968 | Remapped | NW_003571040.1 |
| NW_003571042.1 | Chr8|NW_003571042.1 | 4 | 672 | Remapped | NW_003571042.1 |
| NW_003315931.1 | Chr9|NW_003315931.1 | 1 | 488 | Remapped | NW_003315931.1 |
| NW_004070869.1 | Chr9|NW_004070869.1 | 1 | 59 | Remapped | NW_004070869.1 |
| NW_003315934.1 | Chr10|NW_003315934.1 | 1 | 112 | Remapped | NW_003315934.1 |
| NW_004504302.1 | Chr10|NW_004504302.1 | 1 | 488 | Remapped | NW_004504302.1 |
| NW_003315940.1 | Chr12|NW_003315940.1 | 1 | 486 | Remapped | NW_003315940.1 |
| NW_004166863.1 | Chr14|NW_004166863.1 | 5 | 1,199 | Remapped | NW_004166863.1 |
| NT_167251.1 | Chr17|NT_167251.1 | 1 | 313 | Remapped | NT_167251.1 |
| NW_003315949.1 | Chr17|NW_003315949.1 | 3 | 1,156 | Remapped | NW_003315949.1 |
| NW_003315953.1 | Chr17|NW_003315953.1 | 1 | 53 | Remapped | NW_003315953.1 |
| NW_003871086.1 | Chr17|NW_003871086.1 | 1 | 118 | Remapped | NW_003871086.1 |
| NW_003871092.1 | Chr17|NW_003871092.1 | 1 | 109 | Remapped | NW_003871092.1 |
| NW_003871093.1 | Chr17|NW_003871093.1 | 1 | 400 | Remapped | NW_003871093.1 |
| NW_004070872.2 | Chr17|NW_004070872.2 | 1 | 488 | Remapped | NW_004070872.2 |
| NW_003571053.2 | Chr19|NW_003571053.2 | 1 | 93 | Remapped | NW_003571053.2 |
| NW_003871094.1 | Chr19|NW_003871094.1 | 1 | 488 | Remapped | NW_003871094.1 |
| NW_004166865.1 | Chr19|NW_004166865.1 | 1 | 488 | Remapped | NW_004166865.1 |
| NW_003315968.1 | Chr21|NW_003315968.1 | 1 | 68 | Remapped | NW_003315968.1 |
| NW_003315972.1 | Chr22|NW_003315972.1 | 1 | 140 | Remapped | NW_003315972.1 |
| NW_003871100.1 | ChrX|NW_003871100.1 | 1 | 254 | Remapped | NW_003871100.1 |
| NW_003871103.3 | ChrX|NW_003871103.3 | 2 | 889 | Remapped | NW_003871103.3 |
| NW_004070877.1 | ChrX|NW_004070877.1 | 1 | 269 | Remapped | NW_004070877.1 |
| NW_004070880.2 | ChrX|NW_004070880.2 | 6 | 2,204 | Remapped | NW_004070880.2 |
| NW_004070881.1 | ChrX|NW_004070881.1 | 1 | 259 | Remapped | NW_004070881.1 |
| NW_004070888.1 | ChrX|NW_004070888.1 | 1 | 488 | Remapped | NW_004070888.1 |
| NW_004070890.2 | ChrX|NW_004070890.2 | 6 | 1,369 | Remapped | NW_004070890.2 |
| Sequence ID | Chr | Number of Variant Regions | Number of Variant Calls | Placement type | Link to graphical display |
|---|---|---|---|---|---|
| NC_000001.9 | Chr1 | 86 | 17,390 | Submitted | NC_000001.9 |
| NC_000002.10 | Chr2 | 95 | 16,796 | Submitted | NC_000002.10 |
| NC_000003.10 | Chr3 | 76 | 12,328 | Submitted | NC_000003.10 |
| NC_000004.10 | Chr4 | 100 | 14,200 | Submitted | NC_000004.10 |
| NC_000005.8 | Chr5 | 62 | 10,988 | Submitted | NC_000005.8 |
| NC_000006.10 | Chr6 | 74 | 13,196 | Submitted | NC_000006.10 |
| NC_000007.12 | Chr7 | 69 | 12,679 | Submitted | NC_000007.12 |
| NC_000008.9 | Chr8 | 93 | 18,036 | Submitted | NC_000008.9 |
| NC_000009.10 | Chr9 | 43 | 7,375 | Submitted | NC_000009.10 |
| NC_000010.9 | Chr10 | 50 | 10,071 | Submitted | NC_000010.9 |
| NC_000011.8 | Chr11 | 53 | 8,262 | Submitted | NC_000011.8 |
| NC_000012.10 | Chr12 | 45 | 7,343 | Submitted | NC_000012.10 |
| NC_000013.9 | Chr13 | 30 | 5,332 | Submitted | NC_000013.9 |
| NC_000014.7 | Chr14 | 43 | 10,919 | Submitted | NC_000014.7 |
| NC_000015.8 | Chr15 | 32 | 6,922 | Submitted | NC_000015.8 |
| NC_000016.8 | Chr16 | 32 | 7,668 | Submitted | NC_000016.8 |
| NC_000017.9 | Chr17 | 37 | 9,958 | Submitted | NC_000017.9 |
| NC_000018.8 | Chr18 | 28 | 4,556 | Submitted | NC_000018.8 |
| NC_000019.8 | Chr19 | 20 | 5,370 | Submitted | NC_000019.8 |
| NC_000020.9 | Chr20 | 18 | 3,344 | Submitted | NC_000020.9 |
| NC_000021.7 | Chr21 | 10 | 938 | Submitted | NC_000021.7 |
| NC_000022.9 | Chr22 | 15 | 4,600 | Submitted | NC_000022.9 |
| NC_000023.9 | ChrX | 64 | 18,539 | Submitted | NC_000023.9 |
| NC_000024.8 | ChrY | 8 | 570 | Submitted | NC_000024.8 |
| 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_000001.9 | Chr1 | 86 | 84 | 0 | 1 | 0 | 1 | 17,390 | 16,791 | 0 | 488 | 0 | 111 |
| NC_000002.10 | Chr2 | 95 | 95 | 0 | 0 | 0 | 0 | 16,796 | 16,796 | 0 | 0 | 0 | 0 |
| NC_000003.10 | Chr3 | 76 | 75 | 1 | 0 | 0 | 0 | 12,328 | 11,850 | 478 | 0 | 0 | 0 |
| NC_000004.10 | Chr4 | 100 | 98 | 0 | 0 | 0 | 2 | 14,200 | 13,553 | 0 | 0 | 0 | 647 |
| NC_000005.8 | Chr5 | 62 | 59 | 1 | 1 | 0 | 1 | 10,988 | 9,945 | 475 | 488 | 0 | 80 |
| NC_000006.10 | Chr6 | 74 | 65 | 0 | 0 | 0 | 9 | 13,196 | 10,119 | 0 | 0 | 0 | 3,077 |
| NC_000007.12 | Chr7 | 69 | 65 | 1 | 1 | 0 | 2 | 12,679 | 11,504 | 391 | 207 | 0 | 577 |
| NC_000008.9 | Chr8 | 93 | 88 | 1 | 0 | 0 | 4 | 18,036 | 16,876 | 488 | 0 | 0 | 672 |
| NC_000009.10 | Chr9 | 43 | 41 | 0 | 0 | 0 | 2 | 7,375 | 6,828 | 0 | 0 | 0 | 547 |
| NC_000010.9 | Chr10 | 50 | 47 | 1 | 0 | 0 | 2 | 10,071 | 8,983 | 488 | 0 | 0 | 600 |
| NC_000011.8 | Chr11 | 53 | 53 | 0 | 0 | 0 | 0 | 8,262 | 8,262 | 0 | 0 | 0 | 0 |
| NC_000012.10 | Chr12 | 45 | 44 | 0 | 0 | 0 | 1 | 7,343 | 6,857 | 0 | 0 | 0 | 486 |
| NC_000013.9 | Chr13 | 30 | 30 | 0 | 0 | 0 | 0 | 5,332 | 5,332 | 0 | 0 | 0 | 0 |
| NC_000014.7 | Chr14 | 43 | 38 | 0 | 0 | 0 | 5 | 10,919 | 9,720 | 0 | 0 | 0 | 1,199 |
| NC_000015.8 | Chr15 | 32 | 31 | 1 | 0 | 0 | 0 | 6,922 | 6,434 | 488 | 0 | 0 | 0 |
| NC_000016.8 | Chr16 | 32 | 32 | 0 | 0 | 0 | 0 | 7,668 | 7,668 | 0 | 0 | 0 | 0 |
| NC_000017.9 | Chr17 | 37 | 29 | 0 | 0 | 0 | 8 | 9,958 | 7,809 | 0 | 0 | 0 | 2,149 |
| NC_000018.8 | Chr18 | 28 | 28 | 0 | 0 | 0 | 0 | 4,556 | 4,556 | 0 | 0 | 0 | 0 |
| NC_000019.8 | Chr19 | 20 | 17 | 1 | 0 | 0 | 2 | 5,370 | 4,301 | 488 | 0 | 0 | 581 |
| NC_000020.9 | Chr20 | 18 | 18 | 0 | 0 | 0 | 0 | 3,344 | 3,344 | 0 | 0 | 0 | 0 |
| NC_000021.7 | Chr21 | 10 | 9 | 0 | 0 | 0 | 1 | 938 | 870 | 0 | 0 | 0 | 68 |
| NC_000022.9 | Chr22 | 15 | 14 | 0 | 0 | 0 | 1 | 4,600 | 4,460 | 0 | 0 | 0 | 140 |
| NC_000023.9 | ChrX | 64 | 44 | 1 | 1 | 0 | 18 | 18,539 | 12,082 | 237 | 488 | 0 | 5,732 |
| NC_000024.8 | ChrY | 8 | 8 | 0 | 0 | 0 | 0 | 570 | 570 | 0 | 0 | 0 | 0 |
| 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_000001.9 | Chr1 | 86 | 78 | 2 | 0 | 0 | 6 | 17,390 | 15,356 | 774 | 0 | 0 | 1,260 |
| NC_000002.10 | Chr2 | 95 | 85 | 3 | 0 | 1 | 6 | 16,796 | 14,592 | 161 | 0 | 321 | 1,722 |
| NC_000003.10 | Chr3 | 76 | 73 | 0 | 0 | 0 | 3 | 12,328 | 11,326 | 0 | 0 | 0 | 1,002 |
| NC_000004.10 | Chr4 | 100 | 98 | 0 | 0 | 0 | 2 | 14,200 | 13,553 | 0 | 0 | 0 | 647 |
| NC_000005.8 | Chr5 | 62 | 58 | 1 | 1 | 0 | 2 | 10,988 | 9,204 | 475 | 488 | 0 | 821 |
| NC_000006.10 | Chr6 | 74 | 65 | 0 | 1 | 0 | 8 | 13,196 | 10,119 | 0 | 488 | 0 | 2,589 |
| NC_000007.12 | Chr7 | 69 | 61 | 1 | 0 | 0 | 7 | 12,679 | 9,986 | 391 | 0 | 0 | 2,302 |
| NC_000008.9 | Chr8 | 93 | 79 | 0 | 0 | 0 | 14 | 18,036 | 12,876 | 0 | 0 | 0 | 5,160 |
| NC_000009.10 | Chr9 | 43 | 39 | 1 | 2 | 0 | 1 | 7,375 | 5,840 | 488 | 559 | 0 | 488 |
| NC_000010.9 | Chr10 | 50 | 46 | 1 | 0 | 0 | 3 | 10,071 | 9,248 | 488 | 0 | 0 | 335 |
| NC_000011.8 | Chr11 | 53 | 49 | 1 | 0 | 0 | 3 | 8,262 | 7,565 | 44 | 0 | 0 | 653 |
| NC_000012.10 | Chr12 | 45 | 37 | 0 | 0 | 0 | 8 | 7,343 | 5,785 | 0 | 0 | 0 | 1,558 |
| NC_000013.9 | Chr13 | 30 | 30 | 0 | 0 | 0 | 0 | 5,332 | 5,332 | 0 | 0 | 0 | 0 |
| NC_000014.7 | Chr14 | 43 | 36 | 2 | 0 | 1 | 4 | 10,919 | 9,449 | 334 | 0 | 219 | 917 |
| NC_000015.8 | Chr15 | 32 | 31 | 0 | 0 | 0 | 1 | 6,922 | 6,848 | 0 | 0 | 0 | 74 |
| NC_000016.8 | Chr16 | 32 | 31 | 0 | 0 | 0 | 1 | 7,668 | 7,655 | 0 | 0 | 0 | 13 |
| NC_000017.9 | Chr17 | 37 | 29 | 0 | 0 | 0 | 8 | 9,958 | 7,745 | 0 | 0 | 0 | 2,213 |
| NC_000018.8 | Chr18 | 28 | 26 | 0 | 0 | 1 | 1 | 4,556 | 3,580 | 0 | 0 | 488 | 488 |
| NC_000019.8 | Chr19 | 20 | 18 | 1 | 0 | 0 | 1 | 5,370 | 4,638 | 488 | 0 | 0 | 244 |
| NC_000020.9 | Chr20 | 18 | 16 | 0 | 0 | 0 | 2 | 3,344 | 2,368 | 0 | 0 | 0 | 976 |
| NC_000021.7 | Chr21 | 10 | 9 | 0 | 0 | 0 | 1 | 938 | 870 | 0 | 0 | 0 | 68 |
| NC_000022.9 | Chr22 | 15 | 11 | 1 | 0 | 0 | 3 | 4,600 | 3,511 | 25 | 0 | 0 | 1,064 |
| NC_000023.9 | ChrX | 64 | 52 | 10 | 2 | 0 | 0 | 18,539 | 13,889 | 3,674 | 976 | 0 | 0 |
| NC_000024.8 | ChrY | 8 | 8 | 0 | 0 | 0 | 0 | 570 | 570 | 0 | 0 | 0 | 0 |
Samplesets
Number of Samplesets: 3
- Sampleset ID:
- 1
- Name:
- Initial Samples for Analysis
- Description:
- Samples from five HapMap populations: Utah residents with Northwest European ancestry (CEU), Han Chinese from Beijing (CHB), Japanese from Tokyo (JPT), Maasai from Kinyawa, Kenya (MKK), and Yoruba from Ibadan, Nigeria (YRI)
- Size:
- 487
- Organisms:
- Homo sapiens
- Sampleset Phenotype(s):
- None reported
| Sample ID | Cell Type | Subject ID | Sex | Ethnicity | Subject Age | Subject Phenotype |
|---|---|---|---|---|---|---|
| NA10836 | B-Lymphocyte | NA10836 | Female | UTAH/MORMON | 44 Years | Not reported |
| NA07348 | B-Lymphocyte | NA07348 | Female | UTAH/MORMON | 45 Years | Not reported |
| NA11993 | B-Lymphocyte | NA11993 | Female | UTAH/MORMON | 80 Years | Not reported |
| NA10843 | B-Lymphocyte | NA10843 | Female | UTAH/MORMON | 49 Years | Not reported |
| NA12154 | B-Lymphocyte | NA12154 | Male | UTAH/MORMON | 92 Years | Not reported |
| NA10857 | B-Lymphocyte | NA10857 | Male | UTAH/MORMON | 47 Years | Not reported |
| NA11839 | B-Lymphocyte | NA11839 | Male | UTAH/MORMON | 67 Years | Not reported |
| NA12156 | B-Lymphocyte | NA12156 | Female | UTAH/MORMON | 81 Years | Not reported |
| NA11881 | B-Lymphocyte | NA11881 | Male | UTAH/MORMON | 62 Years | Not reported |
| NA12335 | B-Lymphocyte | NA12335 | Male | UTAH/MORMON | Not reported | |
| NA11831 | B-Lymphocyte | NA11831 | Male | UTAH/MORMON | 73 Years | Not reported |
| NA10830 | B-Lymphocyte | NA10830 | Male | UTAH/MORMON | 66 Years | Not reported |
| NA06993 | B-Lymphocyte | NA06993 | Male | UTAH/MORMON | 74 Years | Not reported |
| NA07014 | B-Lymphocyte | NA07014 | Female | UTAH/MORMON | 39 Years | Not reported |
| NA10856 | B-Lymphocyte | NA10856 | Male | UTAH/MORMON | 46 Years | Not reported |
| NA10840 | B-Lymphocyte | NA10840 | Female | UTAH/MORMON | 42 Years | Not reported |
| NA07048 | B-Lymphocyte | NA07048 | Male | UTAH/MORMON | 43 Years | Not reported |
| NA12056 | B-Lymphocyte | NA12056 | Male | UTAH/MORMON | 79 Years | Not reported |
| NA12236 | B-Lymphocyte | NA12236 | Female | UTAH/MORMON | 86 Years | Not reported |
| NA12275 | B-Lymphocyte | NA12275 | Female | UTAH/MORMON | 69 Years | Not reported |
| NA10845 | B-Lymphocyte | NA10845 | Male | UTAH/MORMON | 49 Years | Not reported |
| NA12155 | B-Lymphocyte | NA12155 | Male | UTAH/MORMON | 86 Years | Not reported |
| NA06995 | B-Lymphocyte | NA06995 | Male | UTAH/MORMON | 45 Years | Not reported |
| NA12146 | B-Lymphocyte | NA12146 | Male | UTAH/MORMON | 61 Years | Not reported |
| NA11917 | B-Lymphocyte | NA11917 | Male | UTAH/MORMON | 66 Years | Not reported |
| NA12286 | B-Lymphocyte | NA12286 | Male | UTAH/MORMON | 70 Years | Not reported |
| NA11920 | B-Lymphocyte | NA11920 | Female | UTAH/MORMON | 66 Years | Not reported |
| NA12249 | B-Lymphocyte | NA12249 | Female | UTAH/MORMON | 77 Years | Not reported |
| NA11830 | B-Lymphocyte | NA11830 | Female | UTAH/MORMON | 63 Years | Not reported |
| NA10837 | B-Lymphocyte | NA10837 | Male | UTAH/MORMON | 43 Years | Not reported |
| NA10859 | B-Lymphocyte | NA10859 | Female | UTAH/MORMON | 41 Years | Not reported |
| NA10838 | B-Lymphocyte | NA10838 | Male | UTAH/MORMON | 60 Years | Not reported |
| NA06991 | B-Lymphocyte | NA06991 | Female | UTAH/MORMON | 42 Years | Not reported |
| NA11843 | B-Lymphocyte | NA11843 | Male | UTAH/MORMON | 77 Years | Not reported |
| NA11995 | B-Lymphocyte | NA11995 | Female | UTAH/MORMON | 84 Years | Not reported |
| NA12336 | B-Lymphocyte | NA12336 | Female | UTAH/MORMON | Not reported | |
| NA06989 | B-Lymphocyte | NA06989 | Female | UTAH/MORMON | 62 Years | Not reported |
| NA10831 | B-Lymphocyte | NA10831 | Female | UTAH/MORMON | 59 Years | Not reported |
| NA11894 | B-Lymphocyte | NA11894 | Female | UTAH/MORMON | 69 Years | Not reported |
| NA11829 | B-Lymphocyte | NA11829 | Male | UTAH/MORMON | 72 Years | Not reported |
| NA11992 | B-Lymphocyte | NA11992 | Male | UTAH/MORMON | 86 Years | Not reported |
| NA10850 | B-Lymphocyte | NA10850 | Female | UTAH/MORMON | 48 Years | Not reported |
| NA12043 | B-Lymphocyte | NA12043 | Male | UTAH/MORMON | 74 Years | Not reported |
| NA07022 | B-Lymphocyte | NA07022 | Male | UTAH/MORMON | 63 Years | Not reported |
| NA12329 | B-Lymphocyte | NA12329 | Female | UTAH/MORMON | Not reported | |
| NA06984 | B-Lymphocyte | NA06984 | Male | UTAH/MORMON | 63 Years | Not reported |
| NA10860 | B-Lymphocyte | NA10860 | Male | UTAH/MORMON | 50 Years | Not reported |
| NA06985 | B-Lymphocyte | NA06985 | Female | UTAH/MORMON | 69 Years | Not reported |
| NA12044 | B-Lymphocyte | NA12044 | Female | UTAH/MORMON | 70 Years | Not reported |
| NA10852 | B-Lymphocyte | NA10852 | Female | UTAH/MORMON | 48 Years | Not reported |
| NA12264 | B-Lymphocyte | NA12264 | Male | UTAH/MORMON | 72 Years | Not reported |
| NA12234 | B-Lymphocyte | NA12234 | Female | UTAH/MORMON | 74 Years | Not reported |
| NA12145 | B-Lymphocyte | NA12145 | Female | UTAH/MORMON | 70 Years | Not reported |
| NA10851 | B-Lymphocyte | NA10851 | Male | UTAH/MORMON | 52 Years | Not reported |
| NA12004 | B-Lymphocyte | NA12004 | Female | UTAH/MORMON | 92 Years | Not reported |
| NA07347 | B-Lymphocyte | NA07347 | Male | UTAH/MORMON | 86 Years | Not reported |
| NA07357 | B-Lymphocyte | NA07357 | Male | UTAH/MORMON | 69 Years | Not reported |
| NA12272 | B-Lymphocyte | NA12272 | Male | UTAH/MORMON | 73 Years | Not reported |
| NA12341 | B-Lymphocyte | NA12341 | Female | UTAH/MORMON | Not reported | |
| NA12283 | B-Lymphocyte | NA12283 | Female | UTAH/MORMON | 64 Years | Not reported |
| NA06994 | B-Lymphocyte | NA06994 | Male | UTAH/MORMON | 68 Years | Not reported |
| NA07349 | B-Lymphocyte | NA07349 | Male | UTAH/MORMON | 49 Years | Not reported |
| NA11919 | B-Lymphocyte | NA11919 | Male | UTAH/MORMON | 67 Years | Not reported |
| NA11930 | B-Lymphocyte | NA11930 | Male | UTAH/MORMON | Not reported | |
| NA11840 | B-Lymphocyte | NA11840 | Female | UTAH/MORMON | 67 Years | Not reported |
| NA12282 | B-Lymphocyte | NA12282 | Male | UTAH/MORMON | 69 Years | Not reported |
| NA07051 | B-Lymphocyte | NA07051 | Male | UTAH/MORMON | 67 Years | Not reported |
| NA10864 | B-Lymphocyte | NA10864 | Female | UTAH/MORMON | 40 Years | Not reported |
| NA11892 | B-Lymphocyte | NA11892 | Female | UTAH/MORMON | 73 Years | Not reported |
| NA07034 | B-Lymphocyte | NA07034 | Male | UTAH/MORMON | 71 Years | Not reported |
| NA11918 | B-Lymphocyte | NA11918 | Female | UTAH/MORMON | 64 Years | Not reported |
| NA12248 | B-Lymphocyte | NA12248 | Male | UTAH/MORMON | 89 Years | Not reported |
| NA11994 | B-Lymphocyte | NA11994 | Male | UTAH/MORMON | 80 Years | Not reported |
| NA07031 | B-Lymphocyte | NA07031 | Female | UTAH/MORMON | 63 Years | Not reported |
| NA12005 | B-Lymphocyte | NA12005 | Male | UTAH/MORMON | 77 Years | Not reported |
| NA11893 | B-Lymphocyte | NA11893 | Male | UTAH/MORMON | 71 Years | Not reported |
| NA06986 | B-Lymphocyte | NA06986 | Male | UTAH/MORMON | 74 Years | Not reported |
| NA10839 | B-Lymphocyte | NA10839 | Female | UTAH/MORMON | 55 Years | Not reported |
| NA10847 | B-Lymphocyte | NA10847 | Female | UTAH/MORMON | 38 Years | Not reported |
| NA12287 | B-Lymphocyte | NA12287 | Female | UTAH/MORMON | 69 Years | Not reported |
| NA12058 | B-Lymphocyte | NA12058 | Female | UTAH/MORMON | 81 Years | Not reported |
| NA12144 | B-Lymphocyte | NA12144 | Male | UTAH/MORMON | 71 Years | Not reported |
| NA12045 | B-Lymphocyte | NA12045 | Male | UTAH/MORMON | 74 Years | Not reported |
| NA07055 | B-Lymphocyte | NA07055 | Female | UTAH/MORMON | 70 Years | Not reported |
| NA10855 | B-Lymphocyte | NA10855 | Female | UTAH/MORMON | 37 Years | Not reported |
| NA10863 | B-Lymphocyte | NA10863 | Female | UTAH/MORMON | 43 Years | Not reported |
| NA07435 | B-Lymphocyte | NA07435 | Male | UTAH/MORMON | 77 Years | Not reported |
| NA11882 | B-Lymphocyte | NA11882 | Female | UTAH/MORMON | 61 Years | Not reported |
| NA07346 | B-Lymphocyte | NA07346 | Female | UTAH/MORMON | 85 Years | Not reported |
| NA07019 | B-Lymphocyte | NA07019 | Female | UTAH/MORMON | 45 Years | Not reported |
| NA10835 | B-Lymphocyte | NA10835 | Male | UTAH/MORMON | 39 Years | Not reported |
| NA12274 | B-Lymphocyte | NA12274 | Male | UTAH/MORMON | 72 Years | Not reported |
| NA12273 | B-Lymphocyte | NA12273 | Female | UTAH/MORMON | 71 Years | Not reported |
| NA07037 | B-Lymphocyte | NA07037 | Female | UTAH/MORMON | 65 Years | Not reported |
| NA07056 | B-Lymphocyte | NA07056 | Female | UTAH/MORMON | 65 Years | Not reported |
| NA12340 | B-Lymphocyte | NA12340 | Male | UTAH/MORMON | Not reported | |
| NA10846 | B-Lymphocyte | NA10846 | Male | UTAH/MORMON | 43 Years | Not reported |
| NA07000 | B-Lymphocyte | NA07000 | Female | UTAH/MORMON | 66 Years | Not reported |
| NA12239 | B-Lymphocyte | NA12239 | Female | UTAH/MORMON | 61 Years | Not reported |
| NA11832 | B-Lymphocyte | NA11832 | Female | UTAH/MORMON | 58 Years | Not reported |
- Sampleset ID:
- 2
- Name:
- Follow-up samples (arrayCGH)
- Description:
- Samples used for follow-up of variants identified in initial samples. These samples are from the following populations: Utah residents with Northwest European ancestry (CEU), Han Chinese from Beijing (CHB), Japanese from Tokyo (JPT), Maasai from Kinyawa, Kenya (MKK), Yoruba from Ibadan, Nigeria (YRI), African American from Southwest USA (ASW), Luhya from Webuye, Kenya (LWK), Mexican American from Los Angeles, CA (MEX), Toscani from Italy (TSI), British from England and Scotland (GBR), Finnish from Finland (FIN), and Han Chinese from South China (CHS)
- Size:
- 947
- Organisms:
- Homo sapiens
- Sampleset Phenotype(s):
- None reported
| Sample ID | Cell Type | Subject ID | Sex | Ethnicity | Subject Phenotype |
|---|---|---|---|---|---|
| HG00126 | B-Lymphocyte | HG00126 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00244 | B-Lymphocyte | HG00244 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00114 | B-Lymphocyte | HG00114 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00173 | B-Lymphocyte | HG00173 | Female | Finnish from Finland (1000 Genomes code: FIN) | Not reported |
| HG00135 | B-Lymphocyte | HG00135 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00234 | B-Lymphocyte | HG00234 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00150 | B-Lymphocyte | HG00150 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00256 | B-Lymphocyte | HG00256 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00179 | B-Lymphocyte | HG00179 | Female | Finnish from Finland (1000 Genomes code: FIN) | Not reported |
| HG00255 | B-Lymphocyte | HG00255 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00152 | B-Lymphocyte | HG00152 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00115 | B-Lymphocyte | HG00115 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00236 | B-Lymphocyte | HG00236 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00148 | B-Lymphocyte | HG00148 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00235 | B-Lymphocyte | HG00235 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00257 | B-Lymphocyte | HG00257 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00113 | B-Lymphocyte | HG00113 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00188 | B-Lymphocyte | HG00188 | Male | Finnish from Finland (1000 Genomes code: FIN) | Not reported |
| HG00185 | B-Lymphocyte | HG00185 | Male | Finnish from Finland (1000 Genomes code: FIN) | Not reported |
| HG00262 | B-Lymphocyte | HG00262 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00157 | B-Lymphocyte | HG00157 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00133 | B-Lymphocyte | HG00133 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00259 | B-Lymphocyte | HG00259 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00177 | B-Lymphocyte | HG00177 | Female | Finnish from Finland (1000 Genomes code: FIN) | Not reported |
| HG00231 | B-Lymphocyte | HG00231 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00130 | B-Lymphocyte | HG00130 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00127 | B-Lymphocyte | HG00127 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00176 | B-Lymphocyte | HG00176 | Female | Finnish from Finland (1000 Genomes code: FIN) | Not reported |
| HG00112 | B-Lymphocyte | HG00112 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00258 | B-Lymphocyte | HG00258 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00247 | B-Lymphocyte | HG00247 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00186 | B-Lymphocyte | HG00186 | Male | Finnish from Finland (1000 Genomes code: FIN) | Not reported |
| HG00181 | B-Lymphocyte | HG00181 | Male | Finnish from Finland (1000 Genomes code: FIN) | Not reported |
| HG00121 | B-Lymphocyte | HG00121 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00124 | B-Lymphocyte | HG00124 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00253 | B-Lymphocyte | HG00253 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00142 | B-Lymphocyte | HG00142 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00254 | B-Lymphocyte | HG00254 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00134 | B-Lymphocyte | HG00134 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00105 | B-Lymphocyte | HG00105 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00250 | B-Lymphocyte | HG00250 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00249 | B-Lymphocyte | HG00249 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00120 | B-Lymphocyte | HG00120 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00138 | B-Lymphocyte | HG00138 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00103 | B-Lymphocyte | HG00103 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00141 | B-Lymphocyte | HG00141 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00240 | B-Lymphocyte | HG00240 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00143 | B-Lymphocyte | HG00143 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00187 | B-Lymphocyte | HG00187 | Male | Finnish from Finland (1000 Genomes code: FIN) | Not reported |
| HG00145 | B-Lymphocyte | HG00145 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00137 | B-Lymphocyte | HG00137 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00132 | B-Lymphocyte | HG00132 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00178 | B-Lymphocyte | HG00178 | Female | Finnish from Finland (1000 Genomes code: FIN) | Not reported |
| HG00118 | B-Lymphocyte | HG00118 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00260 | B-Lymphocyte | HG00260 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00116 | B-Lymphocyte | HG00116 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00243 | B-Lymphocyte | HG00243 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00261 | B-Lymphocyte | HG00261 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00102 | B-Lymphocyte | HG00102 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00245 | B-Lymphocyte | HG00245 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00140 | B-Lymphocyte | HG00140 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00107 | B-Lymphocyte | HG00107 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00264 | B-Lymphocyte | HG00264 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00104 | B-Lymphocyte | HG00104 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00242 | B-Lymphocyte | HG00242 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00190 | B-Lymphocyte | HG00190 | Male | Finnish from Finland (1000 Genomes code: FIN) | Not reported |
| HG00238 | B-Lymphocyte | HG00238 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00128 | B-Lymphocyte | HG00128 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00117 | B-Lymphocyte | HG00117 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00156 | B-Lymphocyte | HG00156 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00263 | B-Lymphocyte | HG00263 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00180 | B-Lymphocyte | HG00180 | Female | Finnish from Finland (1000 Genomes code: FIN) | Not reported |
| HG00237 | B-Lymphocyte | HG00237 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00129 | B-Lymphocyte | HG00129 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00123 | B-Lymphocyte | HG00123 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00246 | B-Lymphocyte | HG00246 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00139 | B-Lymphocyte | HG00139 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00183 | B-Lymphocyte | HG00183 | Male | Finnish from Finland (1000 Genomes code: FIN) | Not reported |
| HG00160 | B-Lymphocyte | HG00160 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00159 | B-Lymphocyte | HG00159 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00109 | B-Lymphocyte | HG00109 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00149 | B-Lymphocyte | HG00149 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00125 | B-Lymphocyte | HG00125 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00232 | B-Lymphocyte | HG00232 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00174 | B-Lymphocyte | HG00174 | Female | Finnish from Finland (1000 Genomes code: FIN) | Not reported |
| HG00122 | B-Lymphocyte | HG00122 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00182 | B-Lymphocyte | HG00182 | Male | Finnish from Finland (1000 Genomes code: FIN) | Not reported |
| HG00110 | B-Lymphocyte | HG00110 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00154 | B-Lymphocyte | HG00154 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00136 | B-Lymphocyte | HG00136 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00251 | B-Lymphocyte | HG00251 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00111 | B-Lymphocyte | HG00111 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00233 | B-Lymphocyte | HG00233 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00189 | B-Lymphocyte | HG00189 | Male | Finnish from Finland (1000 Genomes code: FIN) | Not reported |
| HG00106 | B-Lymphocyte | HG00106 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00252 | B-Lymphocyte | HG00252 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00131 | B-Lymphocyte | HG00131 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00108 | B-Lymphocyte | HG00108 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00119 | B-Lymphocyte | HG00119 | Male | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
| HG00239 | B-Lymphocyte | HG00239 | Female | British from England and Scotland, UK (1000 Genomes codes: GBR) | Not reported |
- Sampleset ID:
- 3
- Name:
- Follow-up samples (PCR and qPCR)
- Description:
- Samples used for PCR and qPCR follow-up of variants identified in the initial samples. These samples are from the Human Genome Diversity Project (HDGP) collection.
- Size:
- 952
- Organisms:
- Homo sapiens
- Sampleset Phenotype(s):
- None reported
| Sample ID | Subject ID | Sex | Ethnicity | Subject Phenotype |
|---|---|---|---|---|
| HGDP00080 | HGDP00080 | Male | Balochi | Not reported |
| HGDP00074 | HGDP00074 | Male | Balochi | Not reported |
| HGDP00108 | HGDP00108 | Male | Hazara | Not reported |
| HGDP00169 | HGDP00169 | Male | Sindhi | Not reported |
| HGDP00144 | HGDP00144 | Male | Makrani | Not reported |
| HGDP00064 | HGDP00064 | Male | Balochi | Not reported |
| HGDP00146 | HGDP00146 | Male | Makrani | Not reported |
| HGDP00099 | HGDP00099 | Male | Hazara | Not reported |
| HGDP00160 | HGDP00160 | Male | Makrani | Not reported |
| HGDP00157 | HGDP00157 | Female | Makrani | Not reported |
| HGDP00027 | HGDP00027 | Male | Brahui | Not reported |
| HGDP00031 | HGDP00031 | Male | Brahui | Not reported |
| HGDP00092 | HGDP00092 | Male | Balochi | Not reported |
| HGDP00019 | HGDP00019 | Male | Brahui | Not reported |
| HGDP00124 | HGDP00124 | Male | Hazara | Not reported |
| HGDP00021 | HGDP00021 | Male | Brahui | Not reported |
| HGDP00158 | HGDP00158 | Male | Makrani | Not reported |
| HGDP00135 | HGDP00135 | Male | Makrani | Not reported |
| HGDP00125 | HGDP00125 | Male | Hazara | Not reported |
| HGDP00005 | HGDP00005 | Male | Brahui | Not reported |
| HGDP00054 | HGDP00054 | Male | Balochi | Not reported |
| HGDP00049 | HGDP00049 | Male | Brahui | Not reported |
| HGDP00116 | HGDP00116 | Male | Hazara | Not reported |
| HGDP00052 | HGDP00052 | Male | Balochi | Not reported |
| HGDP00167 | HGDP00167 | Male | Sindhi | Not reported |
| HGDP00131 | HGDP00131 | Male | Makrani | Not reported |
| HGDP00119 | HGDP00119 | Male | Hazara | Not reported |
| HGDP00082 | HGDP00082 | Male | Balochi | Not reported |
| HGDP00161 | HGDP00161 | Male | Makrani | Not reported |
| HGDP00029 | HGDP00029 | Male | Brahui | Not reported |
| HGDP00127 | HGDP00127 | Male | Hazara | Not reported |
| HGDP00009 | HGDP00009 | Male | Brahui | Not reported |
| HGDP00110 | HGDP00110 | Male | Hazara | Not reported |
| HGDP00045 | HGDP00045 | Male | Brahui | Not reported |
| HGDP00106 | HGDP00106 | Male | Hazara | Not reported |
| HGDP00122 | HGDP00122 | Male | Hazara | Not reported |
| HGDP00150 | HGDP00150 | Male | Makrani | Not reported |
| HGDP00121 | HGDP00121 | Male | Hazara | Not reported |
| HGDP00115 | HGDP00115 | Male | Hazara | Not reported |
| HGDP00118 | HGDP00118 | Male | Hazara | Not reported |
| HGDP00070 | HGDP00070 | Male | Balochi | Not reported |
| HGDP00139 | HGDP00139 | Male | Makrani | Not reported |
| HGDP00041 | HGDP00041 | Male | Brahui | Not reported |
| HGDP00151 | HGDP00151 | Female | Makrani | Not reported |
| HGDP00011 | HGDP00011 | Male | Brahui | Not reported |
| HGDP00086 | HGDP00086 | Male | Balochi | Not reported |
| HGDP00102 | HGDP00102 | Male | Hazara | Not reported |
| HGDP00003 | HGDP00003 | Male | Brahui | Not reported |
| HGDP00163 | HGDP00163 | Male | Sindhi | Not reported |
| HGDP00141 | HGDP00141 | Male | Makrani | Not reported |
| HGDP00076 | HGDP00076 | Male | Balochi | Not reported |
| HGDP00154 | HGDP00154 | Female | Makrani | Not reported |
| HGDP00148 | HGDP00148 | Male | Makrani | Not reported |
| HGDP00047 | HGDP00047 | Male | Brahui | Not reported |
| HGDP00001 | HGDP00001 | Male | Brahui | Not reported |
| HGDP00165 | HGDP00165 | Male | Sindhi | Not reported |
| HGDP00134 | HGDP00134 | Male | Makrani | Not reported |
| HGDP00133 | HGDP00133 | Male | Makrani | Not reported |
| HGDP00155 | HGDP00155 | Female | Makrani | Not reported |
| HGDP00025 | HGDP00025 | Male | Brahui | Not reported |
| HGDP00120 | HGDP00120 | Male | Hazara | Not reported |
| HGDP00090 | HGDP00090 | Male | Balochi | Not reported |
| HGDP00058 | HGDP00058 | Male | Balochi | Not reported |
| HGDP00066 | HGDP00066 | Male | Balochi | Not reported |
| HGDP00137 | HGDP00137 | Male | Makrani | Not reported |
| HGDP00105 | HGDP00105 | Male | Hazara | Not reported |
| HGDP00057 | HGDP00057 | Male | Balochi | Not reported |
| HGDP00094 | HGDP00094 | Male | Balochi | Not reported |
| HGDP00068 | HGDP00068 | Male | Balochi | Not reported |
| HGDP00129 | HGDP00129 | Male | Hazara | Not reported |
| HGDP00007 | HGDP00007 | Male | Brahui | Not reported |
| HGDP00098 | HGDP00098 | Male | Balochi | Not reported |
| HGDP00109 | HGDP00109 | Male | Hazara | Not reported |
| HGDP00078 | HGDP00078 | Male | Balochi | Not reported |
| HGDP00039 | HGDP00039 | Male | Brahui | Not reported |
| HGDP00143 | HGDP00143 | Male | Makrani | Not reported |
| HGDP00130 | HGDP00130 | Male | Makrani | Not reported |
| HGDP00140 | HGDP00140 | Male | Makrani | Not reported |
| HGDP00023 | HGDP00023 | Male | Brahui | Not reported |
| HGDP00062 | HGDP00062 | Male | Balochi | Not reported |
| HGDP00056 | HGDP00056 | Male | Balochi | Not reported |
| HGDP00100 | HGDP00100 | Male | Hazara | Not reported |
| HGDP00136 | HGDP00136 | Male | Makrani | Not reported |
| HGDP00088 | HGDP00088 | Male | Balochi | Not reported |
| HGDP00033 | HGDP00033 | Male | Brahui | Not reported |
| HGDP00017 | HGDP00017 | Male | Brahui | Not reported |
| HGDP00096 | HGDP00096 | Male | Balochi | Not reported |
| HGDP00035 | HGDP00035 | Male | Brahui | Not reported |
| HGDP00060 | HGDP00060 | Male | Balochi | Not reported |
| HGDP00149 | HGDP00149 | Male | Makrani | Not reported |
| HGDP00112 | HGDP00112 | Male | Hazara | Not reported |
| HGDP00103 | HGDP00103 | Male | Hazara | Not reported |
| HGDP00104 | HGDP00104 | Male | Hazara | Not reported |
| HGDP00072 | HGDP00072 | Male | Balochi | Not reported |
| HGDP00037 | HGDP00037 | Male | Brahui | Not reported |
| HGDP00153 | HGDP00153 | Female | Makrani | Not reported |
| HGDP00013 | HGDP00013 | Male | Brahui | Not reported |
| HGDP00145 | HGDP00145 | Male | Makrani | Not reported |
| HGDP00015 | HGDP00015 | Male | Brahui | Not reported |
| HGDP00043 | HGDP00043 | Male | Brahui | Not reported |
Experimental Details
| Experiment ID | Type | Method | Analysis | Platforms | Data | Number of Variant Calls |
|---|---|---|---|---|---|---|
| 1 | Discovery | Oligo aCGH | Probe signal intensity | Agilent Eichler Human CNP 180K v2.1, Agilent Eichler Human CNP 180K v3.0 | GEO | 227,380 |