Lineage-based mutation enrichment analysis for coding genes and noncoding regions.

Mutated genes enriched in Hip versus Lop isolates as assessed from a convergent evolution perspective accounting for lineage adaptation. Lineage enrichment ratio was calculated by dividing lineage-based gene mutation enrichment within Hip variants by that within Lop variants for each gene. Top Hip-linked genes were selected via the following criteria: greater than 2 lineages presenting mutations in that gene in the Hip population and a lineage enrichment ratio greater than 2. (XLSX)