Additional file 3.

Allele frequency of deletions and insertions in 80 genomes. The allele frequencies for deletions (A) and insertions (B), for which there was sufficient read information (see Cao et al.[2] for criteria) in all 80 strains at or 10bp surrounding the indel. They are split by functional annotation classes (obtained from TAIR8). The bars indicate the fractions of indels of each annotation class per allele frequency from all indels of the corresponding annotation class (the total number of indels in an annotation class is denoted in parentheses in the legend labels). Indels overlapping with features of different annotation classes were classified based on following priorities: CDS > UTR > intron > transposon > intergenic. Indels overlapping with coding features were classified based on following priorities: gene loss (for deletions only) > start codon change or loss > splice site change or loss > premature stop codon > stop codon change or loss > in-frame. In-frame indels do not change the frame of the coding sequence. Annotations were performed on each indel without taking into account putative compensating indels or SNPs nearby.

Format: PDF Size: 1.6MB Download file

This file can be viewed with: Adobe Acrobat Reader

Grimm et al. BMC Genomics 2013 14:132   doi:10.1186/1471-2164-14-132