Fig. 4

Coverage (blue) and mapping quality (red) histograms of MinION and PacBio reads mapped to the 649 annotated NLR genes: a MinION 2D pass reads b Adapter trimmed, chimera filtered, corrected MinION 2D pass reads, c PacBio SR, d Adapter trimmed, chimera filtered, PacBio RoI. Approximately 40 contigs are covered with <50× by the MinION 2D and PacBio RoI datasets. For most of the contigs the coverage is ≥50×. For the coverage histograms a cutoff at 1500× was defined. Whereas all datasets are containing some low quality mapping reads indicating ambiguous mapping due to the high similarity of NLR genes, the majority of reads is mapping with a Phred score of 60. As expected PacBio SR and MinION 2D pass reads show a higher number of low quality mapping events as adapter trimmed and chimera filtered PacBio RoI and adapter trimmed, chimera filtered and corrected MinION 2D pass reads