Figure 2. Summary metrics of Variant Call Format file generated using vcf.iobio (Miller et al. ²⁷).

Reference chromosomes are displayed in (a) and the distribution of variants with respect to the reference chromosomes are displayed in (b). The Ts/Tv ratio calculated on the sampled variants is shown in (c). The distribution of the alternative allele frequency (log scale) is shown in (d). Nucleotide substitutions per base is summarised in (e) and the tally of variant types is shown in (f). The distribution of insertion and deletion lengths is shown in (g) and finally the distribution of quality scores, i.e., the QUAL field, is shown in (h).