Second, the qualities of bases supporting the polymorphism had to not be biased toward lower scores compared to those supporting the reference base by a Kolmogorov-Smirnov test (P-value ≥0.05).
Both reference and alternative alleles were expressed in the tumour transcriptome, with nine and seven reads (56% and 44%) supporting the reference and mutant alleles, respectively.
We now recognize these errors because the reads supporting the deletion alleles are much more numerous than the reads supporting the reference sequence alleles.
Reads overlapping each SNV position were extracted from the mapped BAM files and the numbers of reads supporting the reference or alternative allele were counted.
At each site, the number of reads supporting the reference base in cancer and normal is considered to have a binomial distribution.
In the blood genome, eight reads (47%) supported the reference allele G, and nine reads (53%) supported the alternative allele A. In the tumour genome, five sequencing reads (31%) supported the G allele, and eleven reads supported the A allele.
Reference and MEI alleles are defined as follows: any uniquely mapped read pairs spanning the predicted breakpoint with a consistent insert size and orientation will be counted as a fragment supporting the reference allele.
Users may click on one of the green dots representing an instance of allele-specific expression to receive information about the number of reads supporting the reference and variant in whole-genome sequencing and transcriptome sequencing and the statistical significance.
Three genomes deviated from the norm: let-516(h144) is missing both e450 and e61 (all the reads supported the reference sequence); let-388(h88) is missing e61; let-393(has5) has e61, but with a 33% ratio rather than the expected 66%.
