To assess the effect of coverage depth on the sensitivity and specificity of sequence variant detection, genotype calls of the Affymetrix SNP array 6.0 were compared step-wise to the called nucleic acid positions and resulted in an accuracy of more than 99% (Figure S3).
We then analysed the effect of coverage depth on assembly result by varying the amount of sequence data used in assembly.
To assess the effect of coverage depth on the sensitivity and specificity of sequence variant detection, we used genotype calls of an Affymetrix SNP array 6.0 from the cryo material and compared each position to the whole exome sequencing data.
We explored the effect of depth of coverage on calling sequence variants by examining the SNPs, insertions, and deletions identified at a range of coverage depths (5x to 250x).
Figure 6 shows the effect of coverage and population size on assembly for reads of length 100 bp.
We investigated the effect of coverage and quality scores on the frequency threshold (Additional file 1), and found the 0.5% threshold to be stable at coverage's of 10,000 and above, but the threshold does increase below this coverage.
We choose to reflect distinct ranges of genomic depth of coverage (as described in Supplementary Information: the effect of genomic depth of coverage on allele frequency noise).
The compartmental model includes the effect of media coverage on reporting the number of infections as well as the number of individuals successfully vaccinated.
