| description |
Illumina sequence reads were aligned to the wMel reference genome using BWA. Since not all genomes or runs had paired end data, single-ended reads were aligned using default parameters. Wolbachia infection status was determined by attempting to produce a wMel reference-based consensus sequence from each individual line and by examining the mean read depth coverage over the reference-based alignment. When a consensus sequence could not be generated for an individual line using the standard SAMtools pileup pipeline and the mean coverage per bp was estimated to be <1 a line was scored as uninfected. Conversely, when a consensus sequence could be produced and mean coverage was >1, lines were scored as infected with Wolbachia. |
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