Additional file 11 of Genome analyses of four Wolbachia strains and associated mitochondria of Rhagoletis cerasi expose cumulative modularity of cytoplasmic incompatibility factors and cytoplasmic hitchhiking across host populations

Additional file 11. wCer5 variant calling. Reference position refers to the wCer5 genome position after the 57 contigs were joined in order. Reads from two libraries: RcerIZ (all reads) and RcerAS (all reads), were mapped at 97% length and 97% similarity, and RcerIZ and RcerAS were mapped competitively to the genomes of wCer1 and wCer5, and wCer1, wCer2 and wCer5, respectively. Variants were called with a minimum cut-off of 35% so a frequency of 65% for a variant is considered homozygous. Location of SNPs within genes is based on PROKKA annotation, and determination of copy number (single or multiple copy) was based on Orthofinder assessment of orthogroups including wCer5, wMeg and wPip genomes.