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Table 1 The mapping coverage of mitogenomes and genomes of Wolbachia strains obtained from three Rhagoletis cerasi individuals and one Ceratitis capitata individual. Genomes of wCer1, wCer2 and wCer4 were assembled from libraries of individuals which only had one strain. Then these reference genomes were used to competitively map reads of RcerAS to wCer1, wCer2 and wCer5, and reads of RcerIZ to wCer1 and wCer5; all other libraries (and sampled libraries) were mapped to a single Wolbachia strain. Subsampling of total reads was selectively applied to normalise the number of mapped reads for comparison between libraries. Mapping parameters were 97% similarity over 97% length, keeping only properly paired reads

From: 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

Host Species Rhagoletis cerasi C. capitata
Population RcerHB; Bajna, Hungary RcerIZ; Zafferana, Italy RcerAS; Stillfried, Austria Ccap10.3 (WolMed S10.3)
Tissue source (DNA extraction) single pupa (whole individual) single larva (whole individual) single pupa (whole individual) single adult (abdomen)
Wolbachia strain detected by MLST markers wCer1 wCer1; wCer5 wCer1; wCer2; wCer5 wCer4
No. of paired reads after QC 125,415,852 147,147,772 131,385,710 130,835,872
No. paired reads mapped to mtDNA (full library) 19,390,560 1,053,116 39,939,364 31,839,758
Percentage mapped to mtDNA 15.46% 0.72% 30.40% 24.34%
No. paired reads mapped to mtDNA (no. subsampled) 81,548 (530,000) 85,244 (12million) 81,608 (270,000) na
Percentage mapped to mtDNA 15.46% 0.71%% 30.23%% na
No. paired reads mapped to wCer1 (full library) 3,586,116 258,194 1,411,170 na
Percentage mapped to wCer1 2.86% 0.18% 1.08% na
No. paired reads mapped to wCer1 (no. subsampled) 286,212 (10million) na 278,582 (26million) na
Percentage mapped to wCer1 2.86% na 1.07% na
No. paired reads mapped to wCer2 (full library) na na 2,561,484 na
Percentage mapped to wCer2 na na 1.95% na
No. paired reads mapped to wCer2 (no. subsampled) na na 1,697,166 (87million) na
Percentage mapped to wCer2 na na 1.95% na
No. paired reads mapped to wCer4 (full library) na na na 1,701,414
Percentage mapped to wCer4 na na na 1.30%
No. paired reads mapped to wCer5 (full library) na 51,402 191,892 na
Percentage mapped to wCer5 na 0.03% 0.15% na