Table 1.
Control and glioma sequence outputs from AluScan
| Control | Glioma | |
|---|---|---|
| Total initial reads (bp) | 896,661,780 | 1,065,234,324 |
| Initial reads (bp) mapped to GRCh37.p2 | 836,745,196 | 983,798,813 |
| Genomic regions mapped (bp) with coverage ≥ 1 | 58,876,070 | 64,297,421 |
| Reads mapped (bp) with coverage ≥ 10 | 717,228,580 | 853,715,563 |
| Genomic regions mapped with coverage ≥ 10: | ||
| Total regions (bp) | 10,638,683 | 11,846,868 |
| Average depth (x) | 67.4 | 72.1 |
| Inter-Alu sequences mapped (bp) | 10,149,445 | 11,275,690 |
| Genic sequences mapped (bp) | 5,644,023 | 6,274,433 |
| Genic sequences mapped as % of total mapped regions | 53.1% | 53.0% |
| Excess in genic sequencesa | 13.1% | 13.0% |
| Number of genes with mapped region | 8,502 | 9,205 |
| Number of cancer candidate genesb with mapped region | 2,921 | 3,096 |
| Cancer candidate genesb with mapped region as % of genes with mapped region |
34.4% | 33.6% |
| Excess in cancer candidate genesc | 8.4% | 7.6% |
aExcess in % genic sequences with mapped region relative to the 40% genic sequences in the reference human genome.
bCancer candidate genes refer to genes listed in Gene Ranker: TCGA GBM 6000.
cExcess in % cancer candidate genes with mapped region relative to the 26% of total human genes included in Gene Ranker: TCGA GBM 6000.