2.7 Variant calling
SNPs and INDELs (insertions and deletions) were called as previously described (Zimpel, 2020) using samtools mpileup (Li, 2011) and VarScan mpileup2cns (Koboldt et al., 2012) with parameters of minimum read depth of 7, mapping quality and minimum base quality of 20, and strand bias filter on, followed by annotation using SnpEff (Cingolani et al., 2012). INDELs as well as SNPs from repetitive regions (PE/PPE, transposases, integrases, maturase, phage and repetitive family 13E12 genes) were removed from the analysis (Zimpel, 2020). Genomes were excluded if the number of heterogeneous SNPs exceeded 15% of the total number of detected SNPs in a genome.