Additional file 10 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 10. wCer1 variant calling. Reference position refers to the wCer1 genome position after the 16 contigs were joined in order. Reads from three libraries: RcerHB (sampled to 10 million reads), RcerIZ (all reads) and RcerAS (sampled to 26 milion 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% frequency, 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 wCer1, wAu and wMel genomes