As a result, both energy signals and timing triggers from the photodetectors are required to be read out by the front-end ASIC.
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A consent form written in the local language, Chichewa, was required to be read, understood, and signed before an interview commenced.
In addition, the sequence identity over the SNPs is required to be at least 99% to count a read for any allele.
Therefore, when the average cover ratio is required to be 20× for all genes, the required read count will be approximately 1.3 × 10 nucleotides, roughly corresponding to a read count of approximately 1.1 × 10 bases, which was used to derive the distribution for MEFs (Fig. 1B). Figure 1B also indicates some interesting aspects of genome stability of induced pluripotent stem (iPS) cells.
The results were filtered using GATK's VariantFiltration, where in order to pass, read depth was required to be > =5 reads, SNP quality had to be > =50, and no more than 2 SNPs in a 10 base pair window were allowed.
Alternative splice sites were required to be supported by a read number of at least 25% uniquely mapped reads compared to the read number of the surrounding exons.
Indels were required to be present in 5 reads or more in the tumor and not present in the matched normal sample.
Candidate sites were required to be covered by more than 30 reads with at least 25% of reads possessing the alternate allele.
SNPs were required to be covered by at least four quality reads, with at least two reads (for low cover regions) or 20%% of reads supporting the alternate base required for a call of an alternate base.
Using these ratios in the simulation algorithm we found that five to seven reads were required to be 95% confident that both copies had been sequenced.
