nstd40 (Sharp et al. 2006)
- Organism:
- Human
- Study Type:
- Case-Control
- Submitter:
- Andrew Sharp
- Submitter URL:
- http://humanparalogy.gs.washington.edu/structuralvariation/
- Description:
- Based on the duplication architecture of the genome, we investigated 130 regions that we hypothesized as candidates for previously undescribed genomic disorders. We tested 290 individuals with mental retardation by BAC array comparative genomic hybridization and identified 16 pathogenic rearrangements, including de novo microdeletions of 17q21.31 found in four individuals. See Variant Summary counts for nstd40 in dbVar Variant Summary.
- Publication(s):
- Sharp et al. 2006
Detailed Information: Download 689 Variant Regions, Download 5055 Variant Calls, Download Both, FTP
Variant Summary
Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted; Remapped: GRCh37.p13 (hg19)
Submitted: NCBI34 (hg16)
| Sequence ID | Chr | Number of Variant Regions | Number of Variant Calls | Placement type | Link to graphical display |
|---|---|---|---|---|---|
| NC_000001.11 | Chr1 | 51 | 487 | Remapped | NC_000001.11 |
| NC_000002.12 | Chr2 | 24 | 58 | Remapped | NC_000002.12 |
| NC_000003.12 | Chr3 | 15 | 102 | Remapped | NC_000003.12 |
| NC_000004.12 | Chr4 | 28 | 121 | Remapped | NC_000004.12 |
| NC_000005.10 | Chr5 | 42 | 753 | Remapped | NC_000005.10 |
| NC_000006.12 | Chr6 | 24 | 132 | Remapped | NC_000006.12 |
| NC_000007.14 | Chr7 | 54 | 287 | Remapped | NC_000007.14 |
| NC_000008.11 | Chr8 | 24 | 306 | Remapped | NC_000008.11 |
| NC_000009.12 | Chr9 | 52 | 179 | Remapped | NC_000009.12 |
| NC_000010.11 | Chr10 | 15 | 93 | Remapped | NC_000010.11 |
| NC_000011.10 | Chr11 | 23 | 75 | Remapped | NC_000011.10 |
| NC_000012.12 | Chr12 | 16 | 36 | Remapped | NC_000012.12 |
| NC_000013.11 | Chr13 | 11 | 61 | Remapped | NC_000013.11 |
| NC_000014.9 | Chr14 | 7 | 310 | Remapped | NC_000014.9 |
| NC_000015.10 | Chr15 | 52 | 413 | Remapped | NC_000015.10 |
| NC_000016.10 | Chr16 | 38 | 106 | Remapped | NC_000016.10 |
| NC_000017.11 | Chr17 | 64 | 283 | Remapped | NC_000017.11 |
| NC_000018.10 | Chr18 | 5 | 5 | Remapped | NC_000018.10 |
| NC_000019.10 | Chr19 | 29 | 228 | Remapped | NC_000019.10 |
| NC_000020.11 | Chr20 | 8 | 17 | Remapped | NC_000020.11 |
| NC_000021.9 | Chr21 | 7 | 51 | Remapped | NC_000021.9 |
| NC_000022.11 | Chr22 | 34 | 574 | Remapped | NC_000022.11 |
| NC_000023.11 | ChrX | 25 | 161 | Remapped | NC_000023.11 |
| NC_000024.10 | ChrY | 18 | 35 | Remapped | NC_000024.10 |
| NT_187523.1 | Chr2|NT_187523.1 | 1 | 2 | Remapped | NT_187523.1 |
| NT_187525.1 | Chr2|NT_187525.1 | 1 | 1 | Remapped | NT_187525.1 |
| NT_187647.1 | Chr2|NT_187647.1 | 1 | 2 | Remapped | NT_187647.1 |
| NW_012132915.1 | Chr2|NW_012132915.1 | 1 | 20 | Remapped | NW_012132915.1 |
| NT_187678.1 | Chr3|NT_187678.1 | 1 | 43 | Remapped | NT_187678.1 |
| NT_187688.1 | Chr3|NT_187688.1 | 1 | 43 | Remapped | NT_187688.1 |
| NT_187689.1 | Chr3|NT_187689.1 | 1 | 43 | Remapped | NT_187689.1 |
| NT_187690.1 | Chr3|NT_187690.1 | 1 | 43 | Remapped | NT_187690.1 |
| NT_187691.1 | Chr3|NT_187691.1 | 1 | 43 | Remapped | NT_187691.1 |
| NT_187532.1 | Chr3|NT_187532.1 | 1 | 43 | Remapped | NT_187532.1 |
| NT_187649.1 | Chr3|NT_187649.1 | 1 | 43 | Remapped | NT_187649.1 |
| NW_018654711.1 | Chr3|NW_018654711.1 | 1 | 1 | Remapped | NW_018654711.1 |
| NT_187679.1 | Chr4|NT_187679.1 | 1 | 1 | Remapped | NT_187679.1 |
| NT_187547.1 | Chr5|NT_187547.1 | 1 | 1 | Remapped | NT_187547.1 |
| NT_187548.1 | Chr5|NT_187548.1 | 1 | 1 | Remapped | NT_187548.1 |
| NW_003315917.2 | Chr5|NW_003315917.2 | 2 | 60 | Remapped | NW_003315917.2 |
| NW_016107297.1 | Chr5|NW_016107297.1 | 1 | 6 | Remapped | NW_016107297.1 |
| NW_016107298.1 | Chr5|NW_016107298.1 | 1 | 3 | Remapped | NW_016107298.1 |
| NT_187558.1 | Chr7|NT_187558.1 | 1 | 2 | Remapped | NT_187558.1 |
| NT_187561.1 | Chr7|NT_187561.1 | 1 | 1 | Remapped | NT_187561.1 |
| NT_187653.1 | Chr7|NT_187653.1 | 1 | 2 | Remapped | NT_187653.1 |
| NW_017852930.1 | Chr7|NW_017852930.1 | 1 | 3 | Remapped | NW_017852930.1 |
| NW_018654714.1 | Chr7|NW_018654714.1 | 4 | 52 | Remapped | NW_018654714.1 |
| NW_018654715.1 | Chr7|NW_018654715.1 | 1 | 96 | Remapped | NW_018654715.1 |
| NT_187565.1 | Chr8|NT_187565.1 | 1 | 3 | Remapped | NT_187565.1 |
| NT_187569.1 | Chr8|NT_187569.1 | 1 | 1 | Remapped | NT_187569.1 |
| NT_187570.1 | Chr8|NT_187570.1 | 1 | 73 | Remapped | NT_187570.1 |
| NT_187576.1 | Chr8|NT_187576.1 | 2 | 3 | Remapped | NT_187576.1 |
| NT_187654.1 | Chr8|NT_187654.1 | 1 | 3 | Remapped | NT_187654.1 |
| NW_018654717.1 | Chr8|NW_018654717.1 | 5 | 22 | Remapped | NW_018654717.1 |
| NT_187585.1 | Chr11|NT_187585.1 | 1 | 2 | Remapped | NT_187585.1 |
| NW_019805496.1 | Chr11|NW_019805496.1 | 1 | 1 | Remapped | NW_019805496.1 |
| NW_003571049.1 | Chr12|NW_003571049.1 | 1 | 1 | Remapped | NW_003571049.1 |
| NW_011332698.1 | Chr13|NW_011332698.1 | 1 | 44 | Remapped | NW_011332698.1 |
| NW_011332699.1 | Chr13|NW_011332699.1 | 2 | 3 | Remapped | NW_011332699.1 |
| NT_187600.1 | Chr14|NT_187600.1 | 3 | 128 | Remapped | NT_187600.1 |
| NT_187659.1 | Chr15|NT_187659.1 | 1 | 1 | Remapped | NT_187659.1 |
| NT_187660.1 | Chr15|NT_187660.1 | 9 | 74 | Remapped | NT_187660.1 |
| NT_187603.1 | Chr15|NT_187603.1 | 2 | 2 | Remapped | NT_187603.1 |
| NT_187606.1 | Chr15|NT_187606.1 | 2 | 8 | Remapped | NT_187606.1 |
| NW_003315943.1 | Chr15|NW_003315943.1 | 1 | 4 | Remapped | NW_003315943.1 |
| NW_011332701.1 | Chr15|NW_011332701.1 | 7 | 62 | Remapped | NW_011332701.1 |
| NT_187383.1 | Chr16|NT_187383.1 | 2 | 30 | Remapped | NT_187383.1 |
| NT_187607.1 | Chr16|NT_187607.1 | 6 | 19 | Remapped | NT_187607.1 |
| NW_013171813.1 | Chr16|NW_013171813.1 | 1 | 1 | Remapped | NW_013171813.1 |
| NW_017852933.1 | Chr16|NW_017852933.1 | 4 | 11 | Remapped | NW_017852933.1 |
| NW_019805500.1 | Chr16|NW_019805500.1 | 1 | 5 | Remapped | NW_019805500.1 |
| NT_187663.1 | Chr17|NT_187663.1 | 5 | 36 | Remapped | NT_187663.1 |
| NT_167251.2 | Chr17|NT_167251.2 | 5 | 32 | Remapped | NT_167251.2 |
| NT_187614.1 | Chr17|NT_187614.1 | 6 | 8 | Remapped | NT_187614.1 |
| NW_003315952.3 | Chr17|NW_003315952.3 | 1 | 1 | Remapped | NW_003315952.3 |
| NW_017363817.1 | Chr17|NW_017363817.1 | 1 | 1 | Remapped | NW_017363817.1 |
| NW_017363819.1 | Chr17|NW_017363819.1 | 1 | 1 | Remapped | NW_017363819.1 |
| NT_187693.1 | Chr19|NT_187693.1 | 2 | 23 | Remapped | NT_187693.1 |
| NW_003315965.1 | Chr19|NW_003315965.1 | 1 | 1 | Remapped | NW_003315965.1 |
| NT_187629.1 | Chr22|NT_187629.1 | 1 | 22 | Remapped | NT_187629.1 |
| NT_187632.1 | Chr22|NT_187632.1 | 1 | 1 | Remapped | NT_187632.1 |
| NT_187633.1 | Chr22|NT_187633.1 | 1 | 2 | Remapped | NT_187633.1 |
| NW_003315971.2 | Chr22|NW_003315971.2 | 1 | 1 | Remapped | NW_003315971.2 |
| Sequence ID | Chr | Number of Variant Regions | Number of Variant Calls | Placement type | Link to graphical display |
|---|---|---|---|---|---|
| NC_000001.10 | Chr1 | 3 | 3 | Submitted | NC_000001.10 |
| NC_000002.11 | Chr2 | 1 | 1 | Submitted | NC_000002.11 |
| NC_000006.11 | Chr6 | 2 | 2 | Submitted | NC_000006.11 |
| NC_000009.11 | Chr9 | 1 | 1 | Submitted | NC_000009.11 |
| NC_000010.10 | Chr10 | 1 | 1 | Submitted | NC_000010.10 |
| NC_000011.9 | Chr11 | 1 | 1 | Submitted | NC_000011.9 |
| NC_000012.11 | Chr12 | 1 | 1 | Submitted | NC_000012.11 |
| NC_000013.10 | Chr13 | 1 | 1 | Submitted | NC_000013.10 |
| NC_000015.9 | Chr15 | 3 | 3 | Submitted | NC_000015.9 |
| NC_000016.9 | Chr16 | 2 | 2 | Submitted | NC_000016.9 |
| NC_000017.10 | Chr17 | 6 | 6 | Submitted | NC_000017.10 |
| NC_000022.10 | Chr22 | 2 | 2 | Submitted | NC_000022.10 |
| NC_000023.10 | ChrX | 1 | 1 | Submitted | NC_000023.10 |
| NC_000001.10 | Chr1 | 51 | 492 | Remapped | NC_000001.10 |
| NC_000002.11 | Chr2 | 23 | 57 | Remapped | NC_000002.11 |
| NC_000003.11 | Chr3 | 15 | 102 | Remapped | NC_000003.11 |
| NC_000004.11 | Chr4 | 28 | 121 | Remapped | NC_000004.11 |
| NC_000005.9 | Chr5 | 42 | 753 | Remapped | NC_000005.9 |
| NC_000006.11 | Chr6 | 23 | 134 | Remapped | NC_000006.11 |
| NC_000007.13 | Chr7 | 54 | 287 | Remapped | NC_000007.13 |
| NC_000008.10 | Chr8 | 25 | 307 | Remapped | NC_000008.10 |
| NC_000009.11 | Chr9 | 51 | 164 | Remapped | NC_000009.11 |
| NC_000010.10 | Chr10 | 16 | 103 | Remapped | NC_000010.10 |
| NC_000011.9 | Chr11 | 22 | 74 | Remapped | NC_000011.9 |
| NC_000012.11 | Chr12 | 14 | 34 | Remapped | NC_000012.11 |
| NC_000013.10 | Chr13 | 10 | 60 | Remapped | NC_000013.10 |
| NC_000014.8 | Chr14 | 7 | 310 | Remapped | NC_000014.8 |
| NC_000015.9 | Chr15 | 50 | 317 | Remapped | NC_000015.9 |
| NC_000016.9 | Chr16 | 39 | 135 | Remapped | NC_000016.9 |
| NC_000017.10 | Chr17 | 57 | 276 | Remapped | NC_000017.10 |
| NC_000018.9 | Chr18 | 5 | 5 | Remapped | NC_000018.9 |
| NC_000019.9 | Chr19 | 30 | 247 | Remapped | NC_000019.9 |
| NC_000020.10 | Chr20 | 8 | 17 | Remapped | NC_000020.10 |
| NC_000021.8 | Chr21 | 6 | 50 | Remapped | NC_000021.8 |
| NC_000022.10 | Chr22 | 33 | 573 | Remapped | NC_000022.10 |
| NC_000023.10 | ChrX | 24 | 160 | Remapped | NC_000023.10 |
| NC_000024.9 | ChrY | 18 | 35 | Remapped | NC_000024.9 |
| NW_003871055.3 | Chr1|NW_003871055.3 | 6 | 18 | Remapped | NW_003871055.3 |
| NW_003871056.3 | Chr1|NW_003871056.3 | 1 | 1 | Remapped | NW_003871056.3 |
| NW_003871057.1 | Chr1|NW_003871057.1 | 1 | 1 | Remapped | NW_003871057.1 |
| NW_004775427.1 | Chr4|NW_004775427.1 | 1 | 2 | Remapped | NW_004775427.1 |
| NW_003315917.2 | Chr5|NW_003315917.2 | 2 | 60 | Remapped | NW_003315917.2 |
| NW_003571039.1 | Chr7|NW_003571039.1 | 1 | 1 | Remapped | NW_003571039.1 |
| NW_003871064.1 | Chr7|NW_003871064.1 | 6 | 19 | Remapped | NW_003871064.1 |
| NW_004775430.1 | Chr7|NW_004775430.1 | 2 | 3 | Remapped | NW_004775430.1 |
| NW_003571042.1 | Chr8|NW_003571042.1 | 2 | 3 | Remapped | NW_003571042.1 |
| NW_003871068.1 | Chr10|NW_003871068.1 | 2 | 28 | Remapped | NW_003871068.1 |
| NW_003571048.1 | Chr12|NW_003571048.1 | 1 | 1 | Remapped | NW_003571048.1 |
| NW_004166863.1 | Chr14|NW_004166863.1 | 2 | 104 | Remapped | NW_004166863.1 |
| NT_167251.1 | Chr17|NT_167251.1 | 5 | 32 | Remapped | NT_167251.1 |
| NW_003315947.1 | Chr17|NW_003315947.1 | 1 | 16 | Remapped | NW_003315947.1 |
| NW_003315948.2 | Chr17|NW_003315948.2 | 1 | 1 | Remapped | NW_003315948.2 |
| NW_003315949.1 | Chr17|NW_003315949.1 | 2 | 2 | Remapped | NW_003315949.1 |
| NW_003871086.1 | Chr17|NW_003871086.1 | 1 | 47 | Remapped | NW_003871086.1 |
| NW_004070872.2 | Chr17|NW_004070872.2 | 1 | 1 | Remapped | NW_004070872.2 |
| NW_004775433.1 | Chr17|NW_004775433.1 | 1 | 1 | Remapped | NW_004775433.1 |
| NW_003315965.1 | Chr19|NW_003315965.1 | 1 | 1 | Remapped | NW_003315965.1 |
| NW_003871094.1 | Chr19|NW_003871094.1 | 1 | 115 | Remapped | NW_003871094.1 |
| NW_004166865.1 | Chr19|NW_004166865.1 | 1 | 4 | Remapped | NW_004166865.1 |
| NW_003315971.2 | Chr22|NW_003315971.2 | 1 | 1 | Remapped | NW_003315971.2 |
| NW_003871103.3 | ChrX|NW_003871103.3 | 2 | 5 | Remapped | NW_003871103.3 |
| NW_004070880.2 | ChrX|NW_004070880.2 | 4 | 15 | Remapped | NW_004070880.2 |
| NW_004070881.1 | ChrX|NW_004070881.1 | 2 | 4 | Remapped | NW_004070881.1 |
| NW_004070885.1 | ChrX|NW_004070885.1 | 1 | 1 | Remapped | NW_004070885.1 |
| NW_004070887.1 | ChrX|NW_004070887.1 | 2 | 114 | Remapped | NW_004070887.1 |
| NW_004070888.1 | ChrX|NW_004070888.1 | 1 | 1 | Remapped | NW_004070888.1 |
| NW_004070890.2 | ChrX|NW_004070890.2 | 1 | 1 | Remapped | NW_004070890.2 |
| Sequence ID | Chr | Number of Variant Regions | Number of Variant Calls | Placement type | Link to graphical display |
|---|---|---|---|---|---|
| NC_000001.7 | Chr1 | 53 | 494 | Submitted | NC_000001.7 |
| GPC_000000200.1 | Chr2 | 23 | 57 | Submitted | GPC_000000200.1 |
| NC_000003.8 | Chr3 | 15 | 102 | Submitted | NC_000003.8 |
| NC_000004.8 | Chr4 | 28 | 121 | Submitted | NC_000004.8 |
| NC_000005.7 | Chr5 | 44 | 813 | Submitted | NC_000005.7 |
| NC_000006.8 | Chr6 | 23 | 134 | Submitted | NC_000006.8 |
| NC_000007.10 | Chr7 | 55 | 288 | Submitted | NC_000007.10 |
| NC_000008.8 | Chr8 | 25 | 307 | Submitted | NC_000008.8 |
| GPC_000000201.1 | Chr9 | 55 | 190 | Submitted | GPC_000000201.1 |
| NC_000010.7 | Chr10 | 16 | 103 | Submitted | NC_000010.7 |
| NC_000011.7 | Chr11 | 22 | 74 | Submitted | NC_000011.7 |
| NC_000012.8 | Chr12 | 15 | 35 | Submitted | NC_000012.8 |
| NC_000013.8 | Chr13 | 10 | 60 | Submitted | NC_000013.8 |
| NC_000014.6 | Chr14 | 8 | 320 | Submitted | NC_000014.6 |
| NC_000015.7 | Chr15 | 51 | 418 | Submitted | NC_000015.7 |
| NC_000016.7 | Chr16 | 38 | 134 | Submitted | NC_000016.7 |
| NC_000017.8 | Chr17 | 59 | 281 | Submitted | NC_000017.8 |
| NC_000018.7 | Chr18 | 5 | 5 | Submitted | NC_000018.7 |
| NC_000019.8 | Chr19 | 31 | 251 | Submitted | NC_000019.8 |
| NC_000020.8 | Chr20 | 8 | 17 | Submitted | NC_000020.8 |
| NC_000021.6 | Chr21 | 6 | 50 | Submitted | NC_000021.6 |
| NC_000022.7 | Chr22 | 33 | 573 | Submitted | NC_000022.7 |
| NC_000023.7 | ChrX | 24 | 160 | Submitted | NC_000023.7 |
| NC_000024.6 | ChrY | 18 | 35 | Submitted | NC_000024.6 |
| 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_000001.10 | Chr1 | 3 | 0 | 2 | 0 | 1 | 0 | 3 | 0 | 2 | 0 | 1 | 0 |
| NC_000002.11 | Chr2 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 |
| NC_000006.11 | Chr6 | 2 | 0 | 1 | 0 | 0 | 2 | 2 | 0 | 2 | 0 | 0 | 0 |
| NC_000009.11 | Chr9 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 |
| NC_000010.10 | Chr10 | 1 | 0 | 0 | 0 | 0 | 2 | 1 | 0 | 1 | 0 | 0 | 0 |
| NC_000011.9 | Chr11 | 1 | 0 | 0 | 0 | 0 | 2 | 1 | 0 | 1 | 0 | 0 | 0 |
| NC_000012.11 | Chr12 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 |
| NC_000013.10 | Chr13 | 1 | 0 | 0 | 0 | 0 | 2 | 1 | 0 | 1 | 0 | 0 | 0 |
| NC_000015.9 | Chr15 | 3 | 2 | 1 | 0 | 0 | 0 | 3 | 2 | 1 | 0 | 0 | 0 |
| NC_000016.9 | Chr16 | 2 | 0 | 1 | 1 | 0 | 0 | 2 | 0 | 1 | 1 | 0 | 0 |
| NC_000017.10 | Chr17 | 6 | 0 | 5 | 1 | 0 | 0 | 6 | 0 | 5 | 1 | 0 | 0 |
| NC_000022.10 | Chr22 | 2 | 0 | 2 | 0 | 0 | 0 | 2 | 0 | 2 | 0 | 0 | 0 |
| NC_000023.10 | ChrX | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 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 |
| GPC_000000200.1 | Chr2 | 23 | 20 | 1 | 2 | 0 | 0 | 57 | 52 | 1 | 4 | 0 | 0 |
| GPC_000000201.1 | Chr9 | 55 | 34 | 8 | 9 | 4 | 0 | 190 | 88 | 50 | 26 | 26 | 0 |
| NC_000001.7 | Chr1 | 53 | 35 | 6 | 5 | 1 | 6 | 494 | 388 | 9 | 78 | 1 | 18 |
| NC_000003.8 | Chr3 | 15 | 13 | 2 | 0 | 0 | 0 | 102 | 57 | 45 | 0 | 0 | 0 |
| NC_000004.8 | Chr4 | 28 | 25 | 1 | 1 | 0 | 1 | 121 | 99 | 1 | 19 | 0 | 2 |
| NC_000005.7 | Chr5 | 44 | 41 | 3 | 0 | 0 | 0 | 813 | 810 | 3 | 0 | 0 | 0 |
| NC_000006.8 | Chr6 | 23 | 23 | 0 | 0 | 0 | 0 | 134 | 134 | 0 | 0 | 0 | 0 |
| NC_000007.10 | Chr7 | 55 | 37 | 5 | 4 | 0 | 9 | 288 | 170 | 39 | 56 | 0 | 23 |
| NC_000008.8 | Chr8 | 25 | 19 | 2 | 2 | 0 | 2 | 307 | 274 | 3 | 27 | 0 | 3 |
| NC_000010.7 | Chr10 | 16 | 12 | 1 | 1 | 0 | 2 | 103 | 62 | 7 | 6 | 0 | 28 |
| NC_000011.7 | Chr11 | 22 | 20 | 1 | 1 | 0 | 0 | 74 | 66 | 1 | 7 | 0 | 0 |
| NC_000012.8 | Chr12 | 15 | 13 | 1 | 1 | 0 | 0 | 35 | 29 | 5 | 1 | 0 | 0 |
| NC_000013.8 | Chr13 | 10 | 10 | 0 | 0 | 0 | 0 | 60 | 60 | 0 | 0 | 0 | 0 |
| NC_000014.6 | Chr14 | 8 | 5 | 0 | 0 | 1 | 2 | 320 | 206 | 0 | 0 | 10 | 104 |
| NC_000015.7 | Chr15 | 51 | 41 | 5 | 4 | 1 | 0 | 418 | 185 | 121 | 11 | 101 | 0 |
| NC_000016.7 | Chr16 | 38 | 23 | 12 | 2 | 0 | 1 | 134 | 64 | 39 | 8 | 0 | 23 |
| NC_000017.8 | Chr17 | 59 | 39 | 4 | 4 | 1 | 11 | 281 | 129 | 4 | 45 | 4 | 99 |
| NC_000018.7 | Chr18 | 5 | 5 | 0 | 0 | 0 | 0 | 5 | 5 | 0 | 0 | 0 | 0 |
| NC_000019.8 | Chr19 | 31 | 27 | 1 | 1 | 0 | 2 | 251 | 112 | 4 | 19 | 0 | 116 |
| NC_000020.8 | Chr20 | 8 | 8 | 0 | 0 | 0 | 0 | 17 | 17 | 0 | 0 | 0 | 0 |
| NC_000021.6 | Chr21 | 6 | 4 | 2 | 0 | 0 | 0 | 50 | 47 | 3 | 0 | 0 | 0 |
| NC_000022.7 | Chr22 | 33 | 29 | 0 | 3 | 0 | 1 | 573 | 537 | 0 | 35 | 0 | 1 |
| NC_000023.7 | ChrX | 24 | 10 | 0 | 1 | 0 | 13 | 160 | 18 | 0 | 1 | 0 | 141 |
| NC_000024.6 | ChrY | 18 | 15 | 0 | 3 | 0 | 0 | 35 | 31 | 0 | 4 | 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 |
| GPC_000000200.1 | Chr2 | 23 | 16 | 3 | 1 | 0 | 3 | 57 | 29 | 3 | 2 | 0 | 23 |
| GPC_000000201.1 | Chr9 | 55 | 33 | 10 | 9 | 3 | 0 | 190 | 83 | 50 | 46 | 11 | 0 |
| NC_000001.7 | Chr1 | 53 | 28 | 16 | 5 | 4 | 0 | 494 | 331 | 76 | 78 | 9 | 0 |
| NC_000003.8 | Chr3 | 15 | 12 | 1 | 0 | 0 | 2 | 102 | 56 | 2 | 0 | 0 | 44 |
| NC_000004.8 | Chr4 | 28 | 21 | 5 | 1 | 0 | 1 | 121 | 94 | 7 | 19 | 0 | 1 |
| NC_000005.7 | Chr5 | 44 | 36 | 4 | 0 | 0 | 4 | 813 | 741 | 61 | 0 | 0 | 11 |
| NC_000006.8 | Chr6 | 23 | 21 | 1 | 0 | 1 | 0 | 134 | 129 | 1 | 0 | 4 | 0 |
| NC_000007.10 | Chr7 | 55 | 31 | 14 | 1 | 1 | 8 | 288 | 60 | 72 | 1 | 1 | 154 |
| NC_000008.8 | Chr8 | 25 | 13 | 1 | 2 | 0 | 9 | 307 | 178 | 1 | 27 | 0 | 101 |
| NC_000010.7 | Chr10 | 16 | 12 | 2 | 0 | 2 | 0 | 103 | 77 | 15 | 0 | 11 | 0 |
| NC_000011.7 | Chr11 | 22 | 16 | 3 | 1 | 0 | 2 | 74 | 64 | 6 | 1 | 0 | 3 |
| NC_000012.8 | Chr12 | 15 | 13 | 1 | 0 | 0 | 1 | 35 | 29 | 5 | 0 | 0 | 1 |
| NC_000013.8 | Chr13 | 10 | 8 | 1 | 0 | 0 | 1 | 60 | 15 | 1 | 0 | 0 | 44 |
| NC_000014.6 | Chr14 | 8 | 3 | 1 | 0 | 1 | 3 | 320 | 49 | 133 | 0 | 10 | 128 |
| NC_000015.7 | Chr15 | 51 | 30 | 7 | 3 | 0 | 11 | 418 | 104 | 132 | 106 | 0 | 76 |
| NC_000016.7 | Chr16 | 38 | 12 | 11 | 3 | 0 | 12 | 134 | 51 | 36 | 11 | 0 | 36 |
| NC_000017.8 | Chr17 | 59 | 36 | 5 | 2 | 1 | 15 | 281 | 185 | 6 | 38 | 4 | 48 |
| NC_000018.7 | Chr18 | 5 | 4 | 1 | 0 | 0 | 0 | 5 | 4 | 1 | 0 | 0 | 0 |
| NC_000019.8 | Chr19 | 31 | 25 | 5 | 0 | 0 | 1 | 251 | 130 | 120 | 0 | 0 | 1 |
| NC_000020.8 | Chr20 | 8 | 8 | 0 | 0 | 0 | 0 | 17 | 17 | 0 | 0 | 0 | 0 |
| NC_000021.6 | Chr21 | 6 | 4 | 0 | 0 | 0 | 2 | 50 | 47 | 0 | 0 | 0 | 3 |
| NC_000022.7 | Chr22 | 33 | 19 | 7 | 4 | 0 | 3 | 573 | 209 | 232 | 107 | 0 | 25 |
| NC_000023.7 | ChrX | 24 | 11 | 11 | 2 | 0 | 0 | 160 | 21 | 137 | 2 | 0 | 0 |
| NC_000024.6 | ChrY | 18 | 16 | 0 | 2 | 0 | 0 | 35 | 32 | 0 | 3 | 0 | 0 |
Samplesets
Number of Samplesets: 2
- Sampleset ID:
- 1
- Name:
- Control poulation
- Sampleset Type:
- Control
- Description:
- The control population was assayed using an identical protocol and consisted of 269 individuals of European (n = 90), sub-Saharan African (n = 90), Chinese (n = 45) and Japanese (n = 44) ancestry used in the International HapMap Project, and a further 47 individuals of diverse ethnic origin.
- Size:
- 316
- Organisms:
- Homo sapiens
- Sampleset Phenotype(s):
- See phenotypes on samples
| Sample ID | Cell Type | Subject ID | Sex | Ethnicity | Subject Phenotype |
|---|---|---|---|---|---|
| GM17052 | B-lymphocyte | GM17052 | Female | Japanese | None |
| GM10492 | B-lymphocyte | GM10492 | Male | Mbuti | None |
| NA07348 | B-Lymphocyte | NA07348 | Female | UTAH/MORMON | None |
| GM17058 | B-lymphocyte | GM17058 | Female | Japanese | None |
| GM15731 | B-lymphocyte | GM15731 | Female | Czech | None |
| NA11993 | B-Lymphocyte | NA11993 | Female | UTAH/MORMON | None |
| GM10495 | B-lymphocyte | GM10495 | Male | Mbuti | None |
| GM10471 | B-lymphocyte | GM10471 | Female | Biaka | None |
| NA12057 | B-Lymphocyte | NA12057 | Female | UTAH/MORMON | None |
| JK1058B | B-Lymphocyte | JK1058B | Mbuti | None | |
| GM11323 | B-lymphocyte | GM11323 | Female | Chinese | None |
| NA10857 | B-Lymphocyte | NA10857 | Male | UTAH/MORMON | None |
| GM17014 | B-lymphocyte | GM17014 | Male | Chinese | None |
| NA11839 | B-Lymphocyte | NA11839 | Male | UTAH/MORMON | None |
| JK1688B | B-Lymphocyte | JK1688B | Biaka | None | |
| NA11881 | B-Lymphocyte | NA11881 | Male | UTAH/MORMON | None |
| NA11831 | B-Lymphocyte | NA11831 | Male | UTAH/MORMON | None |
| NA10830 | B-Lymphocyte | NA10830 | Male | UTAH/MORMON | None |
| NA06993 | B-Lymphocyte | NA06993 | Male | UTAH/MORMON | None |
| NA10856 | B-Lymphocyte | NA10856 | Male | UTAH/MORMON | None |
| GM15724 | B-lymphocyte | GM15724 | Male | Czech | Not reported |
| GM15725 | B-lymphocyte | GM15725 | Male | Czech | None |
| GM10967 | B-lymphocyte | GM10967 | Female | Amerindian | None |
| NA07048 | B-Lymphocyte | NA07048 | Male | UTAH/MORMON | None |
| NA12056 | B-Lymphocyte | NA12056 | Male | UTAH/MORMON | None |
| GM17059 | B-lymphocyte | GM17059 | Female | Japanese | None |
| JK1051A | B-Lymphocyte | JK1051A | Mbuti | None | |
| NA12146 | B-Lymphocyte | NA12146 | Male | UTAH/MORMON | None |
| GM15729 | B-lymphocyte | GM15729 | Female | Czech | None |
| GM10971 | B-lymphocyte | GM10971 | Male | Amerindian | None |
| JK776 | B-Lymphocyte | JK776 | Biaka | None | |
| NA11830 | B-Lymphocyte | NA11830 | Female | UTAH/MORMON | None |
| NA10859 | B-Lymphocyte | NA10859 | Female | UTAH/MORMON | None |
| NA10838 | B-Lymphocyte | NA10838 | Male | UTAH/MORMON | None |
| NA06991 | B-Lymphocyte | NA06991 | Female | UTAH/MORMON | None |
| GM10976 | B-lymphocyte | GM10976 | Male | Amerindian | None |
| GM16688 | B-lymphocyte | GM16688 | Female | Chinese | None |
| NA11995 | B-Lymphocyte | NA11995 | Female | UTAH/MORMON | None |
| GM11521 | B-lymphocyte | GM11521 | Female | Druze | None |
| GM10496 | B-lymphocyte | GM10496 | Female | Mbuti | None |
| NA10831 | B-Lymphocyte | NA10831 | Female | UTAH/MORMON | None |
| JK1061 | B-Lymphocyte | JK1061 | Mbuti | None | |
| NA11829 | B-Lymphocyte | NA11829 | Male | UTAH/MORMON | None |
| NA11992 | B-Lymphocyte | NA11992 | Male | UTAH/MORMON | None |
| NA12043 | B-Lymphocyte | NA12043 | Male | UTAH/MORMON | None |
| NA12003 | B-Lymphocyte | NA12003 | Male | UTAH/MORMON | None |
| NA07022 | B-Lymphocyte | NA07022 | Male | UTAH/MORMON | None |
| NA10860 | B-Lymphocyte | NA10860 | Male | UTAH/MORMON | None |
| NA06985 | B-Lymphocyte | NA06985 | Female | UTAH/MORMON | None |
| NA12044 | B-Lymphocyte | NA12044 | Female | UTAH/MORMON | None |
| NA12145 | B-Lymphocyte | NA12145 | Female | UTAH/MORMON | None |
| NA10851 | B-Lymphocyte | NA10851 | Male | UTAH/MORMON | None |
| NA12004 | B-Lymphocyte | NA12004 | Female | UTAH/MORMON | None |
| NA07029 | B-Lymphocyte | NA07029 | Male | UTAH/MORMON | None |
| NA07357 | B-Lymphocyte | NA07357 | Male | UTAH/MORMON | None |
| GM15730 | B-lymphocyte | GM15730 | Female | Czech | None |
| GM17020 | B-lymphocyte | GM17020 | Male | Chinese | None |
| NA06994 | B-Lymphocyte | NA06994 | Male | UTAH/MORMON | None |
| GM11776 | B-lymphocyte | GM11776 | Male | Amerindian | None |
| GM10979 | B-lymphocyte | GM10979 | Female | Amerindian | None |
| NA11840 | B-Lymphocyte | NA11840 | Female | UTAH/MORMON | None |
| GM10969 | B-lymphocyte | GM10969 | Male | Amerindian | None |
| GM10970 | B-lymphocyte | GM10970 | Male | Amerindian | None |
| GM16689 | B-lymphocyte | GM16689 | Male | Chinese | None |
| GM10494 | B-lymphocyte | GM10494 | Male | Mbuti | None |
| NA07034 | B-Lymphocyte | NA07034 | Male | UTAH/MORMON | None |
| NA11994 | B-Lymphocyte | NA11994 | Male | UTAH/MORMON | None |
| NA12005 | B-Lymphocyte | NA12005 | Male | UTAH/MORMON | None |
| GM11523 | B-lymphocyte | GM11523 | Female | Druze | None |
| NA07345 | B-Lymphocyte | NA07345 | Female | UTAH/MORMON | None |
| NA10847 | B-Lymphocyte | NA10847 | Female | UTAH/MORMON | None |
| NA10839 | B-Lymphocyte | NA10839 | Female | UTAH/MORMON | None |
| GM17017 | B-lymphocyte | GM17017 | Male | Chinese | None |
| GM15727 | B-lymphocyte | GM15727 | Male | Czech | None |
| GM10469 | B-lymphocyte | GM10469 | Male | Biaka | None |
| GM17016 | B-lymphocyte | GM17016 | Male | Chinese | None |
| NA12006 | B-Lymphocyte | NA12006 | Female | UTAH/MORMON | None |
| GM15732 | B-lymphocyte | GM15732 | Female | Czech | None |
| NA12144 | B-Lymphocyte | NA12144 | Male | UTAH/MORMON | None |
| GM15728 | B-lymphocyte | GM15728 | Male | Czech | None |
| GM10473 | B-lymphocyte | GM10473 | Female | Biaka | None |
| GM15733 | B-lymphocyte | GM15733 | Female | Czech | None |
| GM10472 | B-lymphocyte | GM10472 | Female | Biaka | None |
| GM17015 | B-lymphocyte | GM17015 | Male | Chinese | None |
| NA07055 | B-Lymphocyte | NA07055 | Female | UTAH/MORMON | None |
| NA10863 | B-Lymphocyte | NA10863 | Female | UTAH/MORMON | None |
| NA10855 | B-Lymphocyte | NA10855 | Female | UTAH/MORMON | None |
| NA11882 | B-Lymphocyte | NA11882 | Female | UTAH/MORMON | None |
| NA10854 | B-Lymphocyte | NA10854 | Female | UTAH/MORMON | None |
| NA07019 | B-Lymphocyte | NA07019 | Female | UTAH/MORMON | None |
| GM15726 | B-lymphocyte | GM15726 | Male | Czech | None |
| NA10835 | B-Lymphocyte | NA10835 | Male | UTAH/MORMON | None |
| GM10470 | B-lymphocyte | GM10470 | Male | Biaka | None |
| GM17051 | B-lymphocyte | GM17051 | Female | Japanese | None |
| NA07056 | B-Lymphocyte | NA07056 | Female | UTAH/MORMON | None |
| NA10861 | B-Lymphocyte | NA10861 | Female | UTAH/MORMON | None |
| NA10846 | B-Lymphocyte | NA10846 | Male | UTAH/MORMON | None |
| NA07000 | B-Lymphocyte | NA07000 | Female | UTAH/MORMON | None |
| NA11832 | B-Lymphocyte | NA11832 | Female | UTAH/MORMON | None |
| GM10493 | B-lymphocyte | GM10493 | Female | Mbuti | None |
- Sampleset ID:
- 2
- Name:
- Test population
- Sampleset Type:
- Case
- Description:
- Test population from the UK comprising 290 children and young adults with idiopathic mental retardation with or without associated dysmorphism or congenital anomalies. Approximately 50% of individuals were referred from clinical genetics centers, ~35% from community learning disability teams and ~15% from other sources, such as by referral from hospital neuropediatricians.
- Size:
- 290
- Organisms:
- Homo sapiens
- Sampleset Phenotype(s):
- Intellectual Disability
| Sample ID | Cell Type | Subject ID | Subject Phenotype |
|---|---|---|---|
| test_subject_106 | Whole blood | test_subject_106 | Intellectual Disability |
| test_subject_165 | Whole blood | test_subject_165 | Intellectual Disability |
| test_subject_110 | Whole blood | test_subject_110 | Intellectual Disability |
| IMR45 | Whole blood | IMR45 | Intellectual Disability |
| IMR103 | Whole blood | IMR103 | Intellectual Disability |
| test_subject_158 | Whole blood | test_subject_158 | Intellectual Disability |
| test_subject_149 | Whole blood | test_subject_149 | Intellectual Disability |
| IMR146 | Whole blood | IMR146 | Intellectual Disability |
| test_subject_144 | Whole blood | test_subject_144 | Intellectual Disability |
| IMR213 | Whole blood | IMR213 | Intellectual Disability |
| test_subject_136 | Whole blood | test_subject_136 | Intellectual Disability |
| test_subject_148 | Whole blood | test_subject_148 | Intellectual Disability |
| test_subject_152 | Whole blood | test_subject_152 | Intellectual Disability |
| test_subject_145 | Whole blood | test_subject_145 | Intellectual Disability |
| test_subject_176 | Whole blood | test_subject_176 | Intellectual Disability |
| test_subject_138 | Whole blood | test_subject_138 | Intellectual Disability |
| IMR371 | Whole blood | IMR371 | Intellectual Disability |
| test_subject_133 | Whole blood | test_subject_133 | Intellectual Disability |
| test_subject_123 | Whole blood | test_subject_123 | Intellectual Disability |
| test_subject_124 | Whole blood | test_subject_124 | Intellectual Disability |
| test_subject_164 | Whole blood | test_subject_164 | Intellectual Disability |
| test_subject_118 | Whole blood | test_subject_118 | Intellectual Disability |
| IMR283 | Whole blood | IMR283 | Intellectual Disability |
| IMR298 | Whole blood | IMR298 | Intellectual Disability |
| test_subject_166 | Whole blood | test_subject_166 | Intellectual Disability |
| test_subject_126 | Whole blood | test_subject_126 | Intellectual Disability |
| test_subject_129 | Whole blood | test_subject_129 | Intellectual Disability |
| test_subject_171 | Whole blood | test_subject_171 | Intellectual Disability |
| test_subject_134 | Whole blood | test_subject_134 | Intellectual Disability |
| test_subject_112 | Whole blood | test_subject_112 | Intellectual Disability |
| test_subject_159 | Whole blood | test_subject_159 | Intellectual Disability |
| test_subject_104 | Whole blood | test_subject_104 | Intellectual Disability |
| IMR192 | Whole blood | IMR192 | Intellectual Disability |
| IMR184 | Whole blood | IMR184 | Intellectual Disability |
| test_subject_142 | Whole blood | test_subject_142 | Intellectual Disability |
| test_subject_150 | Whole blood | test_subject_150 | Intellectual Disability |
| test_subject_143 | Whole blood | test_subject_143 | Intellectual Disability |
| test_subject_113 | Whole blood | test_subject_113 | Intellectual Disability |
| test_subject_122 | Whole blood | test_subject_122 | Intellectual Disability |
| test_subject_121 | Whole blood | test_subject_121 | Intellectual Disability |
| test_subject_173 | Whole blood | test_subject_173 | Intellectual Disability |
| test_subject_147 | Whole blood | test_subject_147 | Intellectual Disability |
| test_subject_116 | Whole blood | test_subject_116 | Intellectual Disability |
| IMR338 | Whole blood | IMR338 | Intellectual Disability |
| IMR163 | Whole blood | IMR163 | Intellectual Disability |
| test_subject_146 | Whole blood | test_subject_146 | Intellectual Disability |
| IMR149 | Whole blood | IMR149 | Intellectual Disability |
| test_subject_155 | Whole blood | test_subject_155 | Intellectual Disability |
| IMR379 | Whole blood | IMR379 | Intellectual Disability |
| test_subject_115 | Whole blood | test_subject_115 | Intellectual Disability |
| test_subject_151 | Whole blood | test_subject_151 | Intellectual Disability |
| test_subject_125 | Whole blood | test_subject_125 | Intellectual Disability |
| IMR349 | Whole blood | IMR349 | Intellectual Disability |
| IMR129 | Whole blood | IMR129 | Intellectual Disability |
| test_subject_163 | Whole blood | test_subject_163 | Intellectual Disability |
| IMR96 | Whole blood | IMR96 | Intellectual Disability |
| test_subject_168 | Whole blood | test_subject_168 | Intellectual Disability |
| test_subject_101 | Whole blood | test_subject_101 | Intellectual Disability |
| IMR43 | Whole blood | IMR43 | Intellectual Disability |
| test_subject_120 | Whole blood | test_subject_120 | Intellectual Disability |
| test_subject_162 | Whole blood | test_subject_162 | Intellectual Disability |
| IMR211 | Whole blood | IMR211 | Intellectual Disability |
| test_subject_156 | Whole blood | test_subject_156 | Intellectual Disability |
| IMR332 | Whole blood | IMR332 | Intellectual Disability |
| test_subject_117 | Whole blood | test_subject_117 | Intellectual Disability |
| test_subject_103 | Whole blood | test_subject_103 | Intellectual Disability |
| test_subject_169 | Whole blood | test_subject_169 | Intellectual Disability |
| test_subject_137 | Whole blood | test_subject_137 | Intellectual Disability |
| IMR253 | Whole blood | IMR253 | Intellectual Disability |
| test_subject_172 | Whole blood | test_subject_172 | Intellectual Disability |
| test_subject_108 | Whole blood | test_subject_108 | Intellectual Disability |
| test_subject_175 | Whole blood | test_subject_175 | Intellectual Disability |
| IMR376 | Whole blood | IMR376 | Intellectual Disability |
| test_subject_139 | Whole blood | test_subject_139 | Intellectual Disability |
| test_subject_100 | Whole blood | test_subject_100 | Intellectual Disability |
| test_subject_154 | Whole blood | test_subject_154 | Intellectual Disability |
| test_subject_132 | Whole blood | test_subject_132 | Intellectual Disability |
| IMR255 | Whole blood | IMR255 | Intellectual Disability |
| test_subject_119 | Whole blood | test_subject_119 | Intellectual Disability |
| test_subject_160 | Whole blood | test_subject_160 | Intellectual Disability |
| test_subject_114 | Whole blood | test_subject_114 | Intellectual Disability |
| test_subject_109 | Whole blood | test_subject_109 | Intellectual Disability |
| test_subject_135 | Whole blood | test_subject_135 | Intellectual Disability |
| test_subject_141 | Whole blood | test_subject_141 | Intellectual Disability |
| test_subject_167 | Whole blood | test_subject_167 | Intellectual Disability |
| test_subject_140 | Whole blood | test_subject_140 | Intellectual Disability |
| test_subject_170 | Whole blood | test_subject_170 | Intellectual Disability |
| test_subject_107 | Whole blood | test_subject_107 | Intellectual Disability |
| test_subject_161 | Whole blood | test_subject_161 | Intellectual Disability |
| test_subject_131 | Whole blood | test_subject_131 | Intellectual Disability |
| test_subject_111 | Whole blood | test_subject_111 | Intellectual Disability |
| test_subject_105 | Whole blood | test_subject_105 | Intellectual Disability |
| test_subject_127 | Whole blood | test_subject_127 | Intellectual Disability |
| test_subject_153 | Whole blood | test_subject_153 | Intellectual Disability |
| test_subject_130 | Whole blood | test_subject_130 | Intellectual Disability |
| test_subject_174 | Whole blood | test_subject_174 | Intellectual Disability |
| test_subject_128 | Whole blood | test_subject_128 | Intellectual Disability |
| test_subject_157 | Whole blood | test_subject_157 | Intellectual Disability |
| test_subject_102 | Whole blood | test_subject_102 | Intellectual Disability |
| IMR26 | Whole blood | IMR26 | Intellectual Disability |
Experimental Details
Validations
| Experiment ID | Method | Analysis | Platform | Number of Variant Calls Validated |
|---|---|---|---|---|
| 3 | FISH | Probe signal intensity | 17 | |
| 4 | Oligo aCGH | Probe signal intensity | Custom NimbleGen array | 12 |