nstd195 (Mwapagha et al. 2021)
- Organism:
- Human
- Study Type:
- Collection
- Submitter:
- Lamech Mwapagha
- Description:
- Whole-genome sequencing (WGS) was performed on DNA isolated from tumour biopsies with a histologically confirmed diagnosis of OSSC. Paired-end sequencing was performed on the Illumina HiSeq2000, with 300 bp reads. Reads were aligned to the Homo sapiens reference genome (GRCh37) using ELAND and CASAVA software. Structural variants reported from the alignment were collated with gene loci, using the variant effect predictor of ENSEMBL. The affected genes were subsequently cross-checked against the genetic association database for disease and cancer associations. See Variant Summary counts for nstd195 in dbVar Variant Summary.
- Publication(s):
- Mwapagha et al. 2021
Detailed Information: Download 14750 Variant Regions, Download 19508 Variant Calls, Download Both, FTP
Variant Summary
Assembly used for analysis:
Remapped: GRCh38.p13 (hg38)
Submitted: GRCh37 (hg19)
| Sequence ID | Chr | Number of Variant Regions | Number of Variant Calls | Placement type | Link to graphical display |
|---|---|---|---|---|---|
| NC_000001.11 | Chr1 | 1,190 | 1,581 | Remapped | NC_000001.11 |
| NC_000002.12 | Chr2 | 1,019 | 1,357 | Remapped | NC_000002.12 |
| NC_000003.12 | Chr3 | 963 | 1,258 | Remapped | NC_000003.12 |
| NC_000004.12 | Chr4 | 1,100 | 1,486 | Remapped | NC_000004.12 |
| NC_000005.10 | Chr5 | 583 | 876 | Remapped | NC_000005.10 |
| NC_000006.12 | Chr6 | 665 | 1,014 | Remapped | NC_000006.12 |
| NC_000007.14 | Chr7 | 1,346 | 1,664 | Remapped | NC_000007.14 |
| NC_000008.11 | Chr8 | 677 | 947 | Remapped | NC_000008.11 |
| NC_000009.12 | Chr9 | 720 | 956 | Remapped | NC_000009.12 |
| NC_000010.11 | Chr10 | 881 | 1,136 | Remapped | NC_000010.11 |
| NC_000011.10 | Chr11 | 572 | 763 | Remapped | NC_000011.10 |
| NC_000012.12 | Chr12 | 742 | 915 | Remapped | NC_000012.12 |
| NC_000013.11 | Chr13 | 381 | 527 | Remapped | NC_000013.11 |
| NC_000014.9 | Chr14 | 340 | 435 | Remapped | NC_000014.9 |
| NC_000015.10 | Chr15 | 407 | 509 | Remapped | NC_000015.10 |
| NC_000016.10 | Chr16 | 755 | 889 | Remapped | NC_000016.10 |
| NC_000017.11 | Chr17 | 407 | 537 | Remapped | NC_000017.11 |
| NC_000018.10 | Chr18 | 281 | 416 | Remapped | NC_000018.10 |
| NC_000019.10 | Chr19 | 474 | 560 | Remapped | NC_000019.10 |
| NC_000020.11 | Chr20 | 467 | 584 | Remapped | NC_000020.11 |
| NC_000021.9 | Chr21 | 491 | 550 | Remapped | NC_000021.9 |
| NC_000022.11 | Chr22 | 405 | 486 | Remapped | NC_000022.11 |
| NC_000023.11 | ChrX | 466 | 593 | Remapped | NC_000023.11 |
| NC_000024.10 | ChrY | 190 | 191 | Remapped | NC_000024.10 |
| NT_187364.1 | Chr1|NT_187364.1 | 11 | 14 | Remapped | NT_187364.1 |
| NT_187367.1 | Chr1|NT_187367.1 | 1 | 2 | Remapped | NT_187367.1 |
| NT_187515.1 | Chr1|NT_187515.1 | 20 | 20 | Remapped | NT_187515.1 |
| NT_187516.1 | Chr1|NT_187516.1 | 2 | 2 | Remapped | NT_187516.1 |
| NT_187518.1 | Chr1|NT_187518.1 | 1 | 1 | Remapped | NT_187518.1 |
| NT_187520.1 | Chr1|NT_187520.1 | 13 | 13 | Remapped | NT_187520.1 |
| NT_187646.1 | Chr1|NT_187646.1 | 1 | 1 | Remapped | NT_187646.1 |
| NW_003315905.1 | Chr1|NW_003315905.1 | 1 | 1 | Remapped | NW_003315905.1 |
| NW_009646194.1 | Chr1|NW_009646194.1 | 1 | 2 | Remapped | NW_009646194.1 |
| NW_011332687.1 | Chr1|NW_011332687.1 | 1 | 1 | Remapped | NW_011332687.1 |
| NW_011332688.1 | Chr1|NW_011332688.1 | 3 | 7 | Remapped | NW_011332688.1 |
| NW_012132914.1 | Chr1|NW_012132914.1 | 2 | 2 | Remapped | NW_012132914.1 |
| NW_014040925.1 | Chr1|NW_014040925.1 | 1 | 1 | Remapped | NW_014040925.1 |
| NW_014040927.1 | Chr1|NW_014040927.1 | 2 | 2 | Remapped | NW_014040927.1 |
| NW_017852928.1 | Chr1|NW_017852928.1 | 2 | 3 | Remapped | NW_017852928.1 |
| NW_018654707.1 | Chr1|NW_018654707.1 | 4 | 7 | Remapped | NW_018654707.1 |
| NW_018654708.1 | Chr1|NW_018654708.1 | 1 | 3 | Remapped | NW_018654708.1 |
| NT_187523.1 | Chr2|NT_187523.1 | 1 | 1 | Remapped | NT_187523.1 |
| NT_187524.1 | Chr2|NT_187524.1 | 15 | 18 | Remapped | NT_187524.1 |
| NT_187525.1 | Chr2|NT_187525.1 | 3 | 3 | Remapped | NT_187525.1 |
| NT_187526.1 | Chr2|NT_187526.1 | 4 | 7 | Remapped | NT_187526.1 |
| NT_187528.1 | Chr2|NT_187528.1 | 2 | 2 | Remapped | NT_187528.1 |
| NT_187529.1 | Chr2|NT_187529.1 | 28 | 31 | Remapped | NT_187529.1 |
| NT_187647.1 | Chr2|NT_187647.1 | 1 | 1 | Remapped | NT_187647.1 |
| NT_187648.1 | Chr2|NT_187648.1 | 14 | 18 | Remapped | NT_187648.1 |
| NW_011332689.1 | Chr2|NW_011332689.1 | 2 | 2 | Remapped | NW_011332689.1 |
| NW_012132915.1 | Chr2|NW_012132915.1 | 33 | 36 | Remapped | NW_012132915.1 |
| NW_015495299.1 | Chr2|NW_015495299.1 | 2 | 2 | Remapped | NW_015495299.1 |
| NW_018654710.1 | Chr2|NW_018654710.1 | 2 | 7 | Remapped | NW_018654710.1 |
| NT_187678.1 | Chr3|NT_187678.1 | 16 | 17 | Remapped | NT_187678.1 |
| NT_187688.1 | Chr3|NT_187688.1 | 16 | 17 | Remapped | NT_187688.1 |
| NT_187689.1 | Chr3|NT_187689.1 | 18 | 20 | Remapped | NT_187689.1 |
| NT_187690.1 | Chr3|NT_187690.1 | 16 | 17 | Remapped | NT_187690.1 |
| NT_187691.1 | Chr3|NT_187691.1 | 16 | 17 | Remapped | NT_187691.1 |
| NT_187532.1 | Chr3|NT_187532.1 | 10 | 11 | Remapped | NT_187532.1 |
| NT_187534.1 | Chr3|NT_187534.1 | 1 | 1 | Remapped | NT_187534.1 |
| NT_187537.1 | Chr3|NT_187537.1 | 1 | 3 | Remapped | NT_187537.1 |
| NT_187538.1 | Chr3|NT_187538.1 | 2 | 3 | Remapped | NT_187538.1 |
| NT_187539.1 | Chr3|NT_187539.1 | 7 | 7 | Remapped | NT_187539.1 |
| NT_187649.1 | Chr3|NT_187649.1 | 16 | 17 | Remapped | NT_187649.1 |
| NW_003871060.2 | Chr3|NW_003871060.2 | 1 | 1 | Remapped | NW_003871060.2 |
| NW_009646197.1 | Chr3|NW_009646197.1 | 2 | 2 | Remapped | NW_009646197.1 |
| NW_011332691.1 | Chr3|NW_011332691.1 | 1 | 1 | Remapped | NW_011332691.1 |
| NW_012132916.1 | Chr3|NW_012132916.1 | 1 | 1 | Remapped | NW_012132916.1 |
| NW_019805491.1 | Chr3|NW_019805491.1 | 2 | 2 | Remapped | NW_019805491.1 |
| NT_187679.1 | Chr4|NT_187679.1 | 41 | 59 | Remapped | NT_187679.1 |
| NT_187543.1 | Chr4|NT_187543.1 | 34 | 48 | Remapped | NT_187543.1 |
| NT_187545.1 | Chr4|NT_187545.1 | 6 | 7 | Remapped | NT_187545.1 |
| NT_187650.1 | Chr4|NT_187650.1 | 75 | 93 | Remapped | NT_187650.1 |
| NW_003315915.1 | Chr4|NW_003315915.1 | 1 | 2 | Remapped | NW_003315915.1 |
| NT_187546.1 | Chr5|NT_187546.1 | 2 | 2 | Remapped | NT_187546.1 |
| NT_187547.1 | Chr5|NT_187547.1 | 5 | 5 | Remapped | NT_187547.1 |
| NT_187548.1 | Chr5|NT_187548.1 | 17 | 19 | Remapped | NT_187548.1 |
| NT_187549.1 | Chr5|NT_187549.1 | 1 | 3 | Remapped | NT_187549.1 |
| NT_187651.1 | Chr5|NT_187651.1 | 14 | 15 | Remapped | NT_187651.1 |
| NT_187652.1 | Chr5|NT_187652.1 | 2 | 2 | Remapped | NT_187652.1 |
| NW_003315917.2 | Chr5|NW_003315917.2 | 7 | 7 | Remapped | NW_003315917.2 |
| NW_009646199.1 | Chr5|NW_009646199.1 | 1 | 1 | Remapped | NW_009646199.1 |
| NW_016107297.1 | Chr5|NW_016107297.1 | 3 | 6 | Remapped | NW_016107297.1 |
| NW_016107298.1 | Chr5|NW_016107298.1 | 3 | 3 | Remapped | NW_016107298.1 |
| NT_187692.1 | Chr6|NT_187692.1 | 1 | 1 | Remapped | NT_187692.1 |
| NT_187552.1 | Chr6|NT_187552.1 | 2 | 2 | Remapped | NT_187552.1 |
| NT_187555.1 | Chr6|NT_187555.1 | 1 | 2 | Remapped | NT_187555.1 |
| NW_004166862.2 | Chr6|NW_004166862.2 | 1 | 1 | Remapped | NW_004166862.2 |
| NW_012132918.1 | Chr6|NW_012132918.1 | 1 | 4 | Remapped | NW_012132918.1 |
| NT_187558.1 | Chr7|NT_187558.1 | 2 | 3 | Remapped | NT_187558.1 |
| NT_187559.1 | Chr7|NT_187559.1 | 2 | 2 | Remapped | NT_187559.1 |
| NT_187560.1 | Chr7|NT_187560.1 | 15 | 15 | Remapped | NT_187560.1 |
| NT_187563.1 | Chr7|NT_187563.1 | 1 | 1 | Remapped | NT_187563.1 |
| NT_187564.1 | Chr7|NT_187564.1 | 1 | 2 | Remapped | NT_187564.1 |
| NW_012132919.1 | Chr7|NW_012132919.1 | 2 | 3 | Remapped | NW_012132919.1 |
| NW_017852930.1 | Chr7|NW_017852930.1 | 4 | 4 | Remapped | NW_017852930.1 |
| NW_018654714.1 | Chr7|NW_018654714.1 | 5 | 5 | Remapped | NW_018654714.1 |
| NW_019805493.1 | Chr7|NW_019805493.1 | 7 | 7 | Remapped | NW_019805493.1 |
| NT_187680.1 | Chr8|NT_187680.1 | 1 | 1 | Remapped | NT_187680.1 |
| NT_187565.1 | Chr8|NT_187565.1 | 2 | 2 | Remapped | NT_187565.1 |
| NT_187566.1 | Chr8|NT_187566.1 | 8 | 9 | Remapped | NT_187566.1 |
| NT_187568.1 | Chr8|NT_187568.1 | 2 | 2 | Remapped | NT_187568.1 |
| NT_187570.1 | Chr8|NT_187570.1 | 10 | 10 | Remapped | NT_187570.1 |
| NT_187571.1 | Chr8|NT_187571.1 | 3 | 6 | Remapped | NT_187571.1 |
| NT_187573.1 | Chr8|NT_187573.1 | 4 | 4 | Remapped | NT_187573.1 |
| NT_187574.1 | Chr8|NT_187574.1 | 1 | 2 | Remapped | NT_187574.1 |
| NT_187654.1 | Chr8|NT_187654.1 | 1 | 1 | Remapped | NT_187654.1 |
| NT_187655.1 | Chr8|NT_187655.1 | 6 | 6 | Remapped | NT_187655.1 |
| NW_017852932.1 | Chr8|NW_017852932.1 | 1 | 1 | Remapped | NW_017852932.1 |
| NW_018654717.1 | Chr8|NW_018654717.1 | 55 | 71 | Remapped | NW_018654717.1 |
| NT_187578.1 | Chr9|NT_187578.1 | 2 | 2 | Remapped | NT_187578.1 |
| NW_013171804.1 | Chr9|NW_013171804.1 | 1 | 2 | Remapped | NW_013171804.1 |
| NT_187579.1 | Chr10|NT_187579.1 | 46 | 52 | Remapped | NT_187579.1 |
| NW_003315934.1 | Chr10|NW_003315934.1 | 1 | 1 | Remapped | NW_003315934.1 |
| NW_003315935.1 | Chr10|NW_003315935.1 | 2 | 2 | Remapped | NW_003315935.1 |
| NT_187681.1 | Chr11|NT_187681.1 | 8 | 11 | Remapped | NT_187681.1 |
| NT_187656.1 | Chr11|NT_187656.1 | 5 | 5 | Remapped | NT_187656.1 |
| NT_187657.1 | Chr11|NT_187657.1 | 1 | 1 | Remapped | NT_187657.1 |
| NT_187581.1 | Chr11|NT_187581.1 | 5 | 5 | Remapped | NT_187581.1 |
| NT_187583.1 | Chr11|NT_187583.1 | 1 | 2 | Remapped | NT_187583.1 |
| NT_187584.1 | Chr11|NT_187584.1 | 1 | 1 | Remapped | NT_187584.1 |
| NT_187586.1 | Chr11|NT_187586.1 | 3 | 4 | Remapped | NT_187586.1 |
| NW_003871074.1 | Chr11|NW_003871074.1 | 1 | 1 | Remapped | NW_003871074.1 |
| NW_011332695.1 | Chr11|NW_011332695.1 | 1 | 2 | Remapped | NW_011332695.1 |
| NW_015148966.1 | Chr11|NW_015148966.1 | 11 | 14 | Remapped | NW_015148966.1 |
| NW_019805497.1 | Chr11|NW_019805497.1 | 2 | 4 | Remapped | NW_019805497.1 |
| NT_187658.1 | Chr12|NT_187658.1 | 6 | 10 | Remapped | NT_187658.1 |
| NT_187587.1 | Chr12|NT_187587.1 | 12 | 14 | Remapped | NT_187587.1 |
| NT_187591.1 | Chr12|NT_187591.1 | 1 | 1 | Remapped | NT_187591.1 |
| NW_003315938.1 | Chr12|NW_003315938.1 | 1 | 1 | Remapped | NW_003315938.1 |
| NW_003315939.2 | Chr12|NW_003315939.2 | 4 | 4 | Remapped | NW_003315939.2 |
| NW_003315940.1 | Chr12|NW_003315940.1 | 1 | 1 | Remapped | NW_003315940.1 |
| NW_003315941.1 | Chr12|NW_003315941.1 | 1 | 1 | Remapped | NW_003315941.1 |
| NW_003571050.1 | Chr12|NW_003571050.1 | 5 | 7 | Remapped | NW_003571050.1 |
| NW_011332696.1 | Chr12|NW_011332696.1 | 3 | 3 | Remapped | NW_011332696.1 |
| NW_015148967.1 | Chr12|NW_015148967.1 | 2 | 4 | Remapped | NW_015148967.1 |
| NW_018654718.1 | Chr12|NW_018654718.1 | 4 | 5 | Remapped | NW_018654718.1 |
| NW_018654720.1 | Chr12|NW_018654720.1 | 1 | 4 | Remapped | NW_018654720.1 |
| NW_019805499.1 | Chr12|NW_019805499.1 | 1 | 4 | Remapped | NW_019805499.1 |
| NT_187592.1 | Chr13|NT_187592.1 | 6 | 6 | Remapped | NT_187592.1 |
| NT_187595.1 | Chr13|NT_187595.1 | 1 | 2 | Remapped | NT_187595.1 |
| NW_009646205.1 | Chr13|NW_009646205.1 | 3 | 3 | Remapped | NW_009646205.1 |
| NW_011332699.1 | Chr13|NW_011332699.1 | 23 | 23 | Remapped | NW_011332699.1 |
| NW_013171811.1 | Chr13|NW_013171811.1 | 1 | 1 | Remapped | NW_013171811.1 |
| NT_187601.1 | Chr14|NT_187601.1 | 1 | 1 | Remapped | NT_187601.1 |
| NW_018654722.1 | Chr14|NW_018654722.1 | 3 | 5 | Remapped | NW_018654722.1 |
| NT_187659.1 | Chr15|NT_187659.1 | 7 | 7 | Remapped | NT_187659.1 |
| NT_187660.1 | Chr15|NT_187660.1 | 12 | 17 | Remapped | NT_187660.1 |
| NT_187382.1 | Chr15|NT_187382.1 | 3 | 3 | Remapped | NT_187382.1 |
| NT_187602.1 | Chr15|NT_187602.1 | 5 | 5 | Remapped | NT_187602.1 |
| NT_187604.1 | Chr15|NT_187604.1 | 2 | 2 | Remapped | NT_187604.1 |
| NT_187605.1 | Chr15|NT_187605.1 | 3 | 3 | Remapped | NT_187605.1 |
| NT_187606.1 | Chr15|NT_187606.1 | 3 | 4 | Remapped | NT_187606.1 |
| NW_003315943.1 | Chr15|NW_003315943.1 | 4 | 4 | Remapped | NW_003315943.1 |
| NW_003315944.2 | Chr15|NW_003315944.2 | 1 | 1 | Remapped | NW_003315944.2 |
| NW_012132920.1 | Chr15|NW_012132920.1 | 3 | 3 | Remapped | NW_012132920.1 |
| NT_187607.1 | Chr16|NT_187607.1 | 5 | 8 | Remapped | NT_187607.1 |
| NT_187610.1 | Chr16|NT_187610.1 | 2 | 2 | Remapped | NT_187610.1 |
| NW_013171812.1 | Chr16|NW_013171812.1 | 1 | 1 | Remapped | NW_013171812.1 |
| NW_013171813.1 | Chr16|NW_013171813.1 | 2 | 2 | Remapped | NW_013171813.1 |
| NW_017852933.1 | Chr16|NW_017852933.1 | 3 | 4 | Remapped | NW_017852933.1 |
| NT_187662.1 | Chr17|NT_187662.1 | 2 | 2 | Remapped | NT_187662.1 |
| NT_187664.1 | Chr17|NT_187664.1 | 3 | 3 | Remapped | NT_187664.1 |
| NT_187611.1 | Chr17|NT_187611.1 | 1 | 1 | Remapped | NT_187611.1 |
| NT_187612.1 | Chr17|NT_187612.1 | 3 | 3 | Remapped | NT_187612.1 |
| NT_187613.1 | Chr17|NT_187613.1 | 7 | 7 | Remapped | NT_187613.1 |
| NT_187615.1 | Chr17|NT_187615.1 | 2 | 2 | Remapped | NT_187615.1 |
| NW_003315952.3 | Chr17|NW_003315952.3 | 5 | 5 | Remapped | NW_003315952.3 |
| NW_003315954.1 | Chr17|NW_003315954.1 | 2 | 3 | Remapped | NW_003315954.1 |
| NW_003315955.1 | Chr17|NW_003315955.1 | 1 | 3 | Remapped | NW_003315955.1 |
| NW_017363817.1 | Chr17|NW_017363817.1 | 4 | 4 | Remapped | NW_017363817.1 |
| NT_187665.1 | Chr18|NT_187665.1 | 1 | 1 | Remapped | NT_187665.1 |
| NT_187666.1 | Chr18|NT_187666.1 | 5 | 5 | Remapped | NT_187666.1 |
| NT_187618.1 | Chr18|NT_187618.1 | 1 | 1 | Remapped | NT_187618.1 |
| NW_003315956.1 | Chr18|NW_003315956.1 | 1 | 3 | Remapped | NW_003315956.1 |
| NW_003315959.1 | Chr18|NW_003315959.1 | 1 | 2 | Remapped | NW_003315959.1 |
| NW_003315961.1 | Chr18|NW_003315961.1 | 5 | 5 | Remapped | NW_003315961.1 |
| NW_013171814.1 | Chr18|NW_013171814.1 | 1 | 1 | Remapped | NW_013171814.1 |
| NW_019805503.1 | Chr18|NW_019805503.1 | 1 | 4 | Remapped | NW_019805503.1 |
| NW_003571061.2 | Chr19|NW_003571061.2 | 6 | 8 | Remapped | NW_003571061.2 |
| NW_003571057.2 | Chr19|NW_003571057.2 | 5 | 5 | Remapped | NW_003571057.2 |
| NW_003571058.2 | Chr19|NW_003571058.2 | 5 | 5 | Remapped | NW_003571058.2 |
| NW_003571059.2 | Chr19|NW_003571059.2 | 5 | 5 | Remapped | NW_003571059.2 |
| NW_003571060.1 | Chr19|NW_003571060.1 | 9 | 10 | Remapped | NW_003571060.1 |
| NW_003571056.2 | Chr19|NW_003571056.2 | 5 | 5 | Remapped | NW_003571056.2 |
| NW_003571055.2 | Chr19|NW_003571055.2 | 6 | 8 | Remapped | NW_003571055.2 |
| NT_187619.1 | Chr19|NT_187619.1 | 1 | 1 | Remapped | NT_187619.1 |
| NT_187620.1 | Chr19|NT_187620.1 | 2 | 2 | Remapped | NT_187620.1 |
| NT_187622.1 | Chr19|NT_187622.1 | 4 | 4 | Remapped | NT_187622.1 |
| NW_003315962.1 | Chr19|NW_003315962.1 | 7 | 8 | Remapped | NW_003315962.1 |
| NW_003315964.2 | Chr19|NW_003315964.2 | 3 | 6 | Remapped | NW_003315964.2 |
| NW_003315965.1 | Chr19|NW_003315965.1 | 2 | 2 | Remapped | NW_003315965.1 |
| NW_003571054.1 | Chr19|NW_003571054.1 | 10 | 13 | Remapped | NW_003571054.1 |
| NW_014040929.1 | Chr19|NW_014040929.1 | 3 | 3 | Remapped | NW_014040929.1 |
| NT_187623.1 | Chr20|NT_187623.1 | 3 | 5 | Remapped | NT_187623.1 |
| NT_187624.1 | Chr20|NT_187624.1 | 4 | 4 | Remapped | NT_187624.1 |
| NW_003315966.2 | Chr20|NW_003315966.2 | 1 | 2 | Remapped | NW_003315966.2 |
| NT_187626.1 | Chr21|NT_187626.1 | 3 | 3 | Remapped | NT_187626.1 |
| NT_187628.1 | Chr21|NT_187628.1 | 1 | 1 | Remapped | NT_187628.1 |
| NT_187629.1 | Chr22|NT_187629.1 | 2 | 2 | Remapped | NT_187629.1 |
| NT_187630.1 | Chr22|NT_187630.1 | 6 | 7 | Remapped | NT_187630.1 |
| NT_187632.1 | Chr22|NT_187632.1 | 5 | 5 | Remapped | NT_187632.1 |
| NT_187667.1 | ChrX|NT_187667.1 | 9 | 10 | Remapped | NT_187667.1 |
| NW_017363820.1 | ChrX|NW_017363820.1 | 1 | 2 | Remapped | NW_017363820.1 |
| NT_187634.1 | ChrX|NT_187634.1 | 9 | 10 | Remapped | NT_187634.1 |
| Sequence ID | Chr | Number of Variant Regions | Number of Variant Calls | Placement type | Link to graphical display |
|---|---|---|---|---|---|
| NC_000001.10 | Chr1 | 1,423 | 1,849 | Submitted | NC_000001.10 |
| NC_000002.11 | Chr2 | 1,056 | 1,405 | Submitted | NC_000002.11 |
| NC_000003.11 | Chr3 | 961 | 1,256 | Submitted | NC_000003.11 |
| NC_000004.11 | Chr4 | 1,100 | 1,486 | Submitted | NC_000004.11 |
| NC_000005.9 | Chr5 | 583 | 876 | Submitted | NC_000005.9 |
| NC_000006.11 | Chr6 | 665 | 1,014 | Submitted | NC_000006.11 |
| NC_000007.13 | Chr7 | 1,347 | 1,665 | Submitted | NC_000007.13 |
| NC_000008.10 | Chr8 | 691 | 961 | Submitted | NC_000008.10 |
| NC_000009.11 | Chr9 | 733 | 975 | Submitted | NC_000009.11 |
| NC_000010.10 | Chr10 | 881 | 1,136 | Submitted | NC_000010.10 |
| NC_000011.9 | Chr11 | 572 | 763 | Submitted | NC_000011.9 |
| NC_000012.11 | Chr12 | 746 | 919 | Submitted | NC_000012.11 |
| NC_000013.10 | Chr13 | 382 | 528 | Submitted | NC_000013.10 |
| NC_000014.8 | Chr14 | 340 | 435 | Submitted | NC_000014.8 |
| NC_000015.9 | Chr15 | 411 | 513 | Submitted | NC_000015.9 |
| NC_000016.9 | Chr16 | 757 | 893 | Submitted | NC_000016.9 |
| NC_000017.10 | Chr17 | 438 | 569 | Submitted | NC_000017.10 |
| NC_000018.9 | Chr18 | 281 | 416 | Submitted | NC_000018.9 |
| NC_000019.9 | Chr19 | 476 | 563 | Submitted | NC_000019.9 |
| NC_000020.10 | Chr20 | 467 | 584 | Submitted | NC_000020.10 |
| NC_000021.8 | Chr21 | 487 | 546 | Submitted | NC_000021.8 |
| NC_000022.10 | Chr22 | 396 | 471 | Submitted | NC_000022.10 |
| NC_000023.10 | ChrX | 467 | 594 | Submitted | NC_000023.10 |
| NC_000024.9 | ChrY | 190 | 191 | Submitted | NC_000024.9 |
| 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 | 1,423 | 1,058 | 186 | 11 | 6 | 273 | 1,849 | 1,454 | 202 | 11 | 6 | 287 |
| NC_000002.11 | Chr2 | 1,056 | 773 | 27 | 14 | 1 | 381 | 1,405 | 1,099 | 32 | 16 | 1 | 397 |
| NC_000003.11 | Chr3 | 961 | 772 | 4 | 0 | 0 | 340 | 1,256 | 1,062 | 4 | 0 | 0 | 345 |
| NC_000004.11 | Chr4 | 1,100 | 824 | 8 | 0 | 0 | 487 | 1,486 | 1,182 | 8 | 0 | 0 | 515 |
| NC_000005.9 | Chr5 | 583 | 492 | 0 | 0 | 0 | 134 | 876 | 777 | 0 | 0 | 0 | 142 |
| NC_000006.11 | Chr6 | 665 | 584 | 17 | 6 | 0 | 108 | 1,014 | 928 | 18 | 6 | 0 | 112 |
| NC_000007.13 | Chr7 | 1,347 | 1,123 | 26 | 15 | 0 | 324 | 1,665 | 1,434 | 27 | 18 | 0 | 327 |
| NC_000008.10 | Chr8 | 691 | 533 | 9 | 6 | 0 | 198 | 961 | 781 | 9 | 6 | 0 | 220 |
| NC_000009.11 | Chr9 | 733 | 536 | 32 | 8 | 1 | 308 | 975 | 761 | 44 | 12 | 1 | 309 |
| NC_000010.10 | Chr10 | 881 | 760 | 5 | 5 | 0 | 176 | 1,136 | 1,005 | 6 | 8 | 0 | 182 |
| NC_000011.9 | Chr11 | 572 | 491 | 9 | 2 | 0 | 118 | 763 | 672 | 9 | 5 | 0 | 125 |
| NC_000012.11 | Chr12 | 746 | 593 | 3 | 0 | 4 | 243 | 919 | 750 | 3 | 0 | 4 | 259 |
| NC_000013.10 | Chr13 | 382 | 262 | 1 | 1 | 0 | 219 | 528 | 407 | 1 | 1 | 0 | 220 |
| NC_000014.8 | Chr14 | 340 | 281 | 0 | 2 | 0 | 101 | 435 | 366 | 0 | 5 | 0 | 108 |
| NC_000015.9 | Chr15 | 411 | 306 | 7 | 0 | 0 | 160 | 513 | 402 | 7 | 0 | 0 | 166 |
| NC_000016.9 | Chr16 | 757 | 638 | 2 | 0 | 2 | 217 | 893 | 768 | 2 | 0 | 4 | 221 |
| NC_000017.10 | Chr17 | 438 | 277 | 6 | 5 | 4 | 247 | 569 | 393 | 9 | 7 | 4 | 257 |
| NC_000018.9 | Chr18 | 281 | 238 | 0 | 0 | 0 | 73 | 416 | 366 | 0 | 0 | 0 | 80 |
| NC_000019.9 | Chr19 | 476 | 369 | 9 | 1 | 0 | 155 | 563 | 444 | 13 | 1 | 0 | 163 |
| NC_000020.10 | Chr20 | 467 | 286 | 0 | 0 | 0 | 354 | 584 | 400 | 0 | 0 | 0 | 357 |
| NC_000021.8 | Chr21 | 487 | 374 | 3 | 0 | 0 | 208 | 546 | 432 | 4 | 0 | 0 | 208 |
| NC_000022.10 | Chr22 | 396 | 340 | 9 | 1 | 0 | 83 | 471 | 410 | 9 | 4 | 0 | 85 |
| NC_000023.10 | ChrX | 467 | 398 | 17 | 6 | 1 | 80 | 594 | 522 | 17 | 7 | 1 | 82 |
| NC_000024.9 | ChrY | 190 | 94 | 0 | 0 | 0 | 179 | 191 | 94 | 0 | 0 | 0 | 180 |
Samplesets
Number of Samplesets: 1
- Name:
- WGS DNA biopsies from oesophageal cancer patients
- Sampleset Type:
- Case
- Description:
- WGS DNA biopsies
- Size:
- 4
- Organisms:
- Homo sapiens
- Sampleset Phenotype(s):
- None reported
| Sample ID | Cell Type | Subject ID | Sex | Ethnicity | Subject Phenotype |
|---|---|---|---|---|---|
| M456 | Oesophageal Cells | M456 | Male | Mixed Ancestry- South Africa | Not reported |
| B381 | Oesophageal Cells | B381 | Male | Black - South Africa | Not reported |
| B450 | Oesophageal Cells | B450 | Female | Black - South Africa | Not reported |
| M478 | Oesophageal Cells | M478 | Female | Mixed Ancestry- South Africa | Not reported |
Experimental Details
| Experiment ID | Type | Method | Analysis | Platforms | Number of Variant Calls |
|---|---|---|---|---|---|
| 1 | Discovery | Sequencing | Paired-end mapping | Illumina HiSeq2000 | 19,508 |