Figure 5.

Percentage of parental origin labels in the single reference pipeline compared with the multi-alignment pipeline. The single-reference labels were generated after alignment by checking the alignment for strain-specific alleles. We removed non-autosome mappings, multi-mapped reads and reads filtered by the Random filter. In general, each strain category gains ∼5% in the multi-alignment pipeline that can be broken down into ∼2% from reads that did not map and ∼3% that were ‘Can’t tell’ in the single-reference pipeline.