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It includes chromosome, start, end, and median coverage of each element.
We achieved a median coverage of 104× (median tumor coverage 98×; median normal coverage 110×).
For 'TAPS (down-sampled)', random reads out of all mapped TAPS reads were selected so that the median coverage matched the median coverage of WGBS.
according to standard Illumina operation procedures with the yield of >14Gb and median coverage of 33-41x.
The top 100 recurrently mutated loci in TCGA lung adenocarcinomas (Fig. 3a) had a median coverage of 3% (i.e. mutated in 3% of TCGA patients).
However, a 400-mutation panel gives a median coverage of 7.9 mutations per patient (Fig. 3b, right panel) with 82.8% patients covered by at least one mutation and 57.6% of patients covered by two or more mutations.
Similar(7)
We reconstructed the genomes of 110 individuals from the wild-type population and of 106 from the recq4a population; these had average and median coverages of 0.6x and of 0.4x.
In contrast the Wald intervals are slightly liberal even for a case-control ratio of 1 2 (median coverage probability of 93% for the Wald and 94% for the Wald-cc interval), and become very liberal for a case-control ratio of 1 9 (median coverage 76% respectively 78%).
This sample was sequenced to a median coverage depth of 91X as part of the Melbourne Genomics Health Alliance demonstration project.
However, the LT has still a median coverage probability of 95% for a case-control ratio of 1 2, and becomes slightly liberal for a case-control ratio of 1 9.
The normalized counts were obtained by subtracting the per-bin coverage counts from the GC correction minus the median coverage count of the sample.
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