Fig 1. Enrichment analyses of variants in gene categories.

(a) Essential, (b) ABR-conferring, (c) Essential and ABR-conferring, and (d) Dispensable and ABR-conferring. The variant enrichment was calculated as the ratio of the proportion of genes with variants in a gene category and the proportion of genes with variants outside the gene category. For example, three essential genes (0.6% of all essential genes) have short indels and the remaining short indels occur in 94 dispensable genes (3.3% of all dispensable genes), which results in a variant ratio of short indels in essential genes of 0.25, i.e., a fourfold depletion. Significant enrichment or depletion, marked by a star, was assessed using Fisher’s exact test (p-value < 0.05, corrected for false discovery rate (FDR), S3 Table).