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Table 1 Control and glioma sequence outputs from AluScan

From: AluScan: a method for genome-wide scanning of sequence and structure variations in the human genome

  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%
  1. aExcess in % genic sequences with mapped region relative to the 40% genic sequences in the reference human genome.
  2. bCancer candidate genes refer to genes listed in Gene Ranker: TCGA GBM 6000.
  3. cExcess in % cancer candidate genes with mapped region relative to the 26% of total human genes included in Gene Ranker: TCGA GBM 6000.