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Figure 6 | BMC Genomics

Figure 6

From: Improving ancient DNA read mapping against modern reference genomes

Figure 6

Nucleotide misincorporation patterns observed following different filtering procedures for human sequences. Helicos and Illumina sequencing reads recovered from the sample showing infinite radiocarbon date were aligned using different combinations of mapping parameters using the BWA aligner. Reads were considered of high-quality when mapping uniquely to the equCab2 genome but not against the human genome (assembly hg19) and showing mapping qualities of at least 25. In a first mapping procedure (Panel A), reads were considered of high-quality when mapping uniquely to the EquCab2 genome but not against the human genome (assembly hg19). In a second mapping procedure (Panel B), reads were considered of high-quality when mapping uniquely to the EquCab2 genome as long as no hit was observed against the human genome (assembly hg19) or as long as the edit distance to the horse genome was lower than the edit distance to the human genome. High-quality reads presented minimal mapping qualities of 25. Nucleotide misincorporation patterns were plotted following mapping with the optimized set of BWA parameters for different subsets of reads. Panel A: Alignments against the horse reference genome, excluding any read that also map against the human reference genome (first column); alignments against the horse reference genome, for reads that also map against the human reference genome (second column); alignments against the human reference genome, for reads that also map against the horse reference genome (third column); alignments against the human reference genome, excluding any read that also maps against the horse reference genome (last column). Panel B: reads showing hits to the horse reference genome only (first column); reads showing hits to the horse and the human reference genomes, and that were filtered in the filtering procedure presented on Panel A (second column); reads showing hits to the horse and the human reference genomes but a lower edit distance to the horse genome (third column); reads showing hits to the horse and the human reference genomes but a lower or equal edit distance to the human genome (last column). Red: C → T. Blue: G → A. Pink: Insertions. Green: Deletions. Orange: Clipped bases. Grey: Other misincorporations.

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