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. 2015 Sep 3;10(9):e0137549. doi: 10.1371/journal.pone.0137549

Fig 4. Read mapping with an incomplete genomic reference sequence.

Fig 4

Exon capture reads were mapped to the Ensembl reference containing progressively fewer homoeologues of the TaGA20ox1 gene. (A) The relevant region of the second exon of TaGA20ox1 is shown, indicating bases that differ between homoeologues (coloured bases) and the G>A mutation in TaGA20ox-A1 (green box). Relevant regions of the BAM files of captured reads from line C6 mapping to (B) TaGA20ox-A1 and (C) TaGA20ox-D1 are shown with variant bases highlighted (G = brown, A = green, C = blue, T = red). Key: a—variant reads from TaGA20ox-A1 in line C6 correctly mapping to the TaGA20ox-A1 target; b—dilution of variant reads by mis-mapped homoeologous reads from homoeologues B and D; c,d—mis-mapped wild-type reads from homoeologues B and D respectively; e—variant reads from homoeologue A mis-mapped to TaGA20ox-D1; f—wild-type reads from homoeologue A mis-mapped to TaGA20ox-D1.