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Figure 7 | BMC Genomics

Figure 7

From: Improving ancient DNA read mapping against modern reference genomes

Figure 7

Divergence estimates based on different mapping and filtering procedures. Illumina reads recovered from the sample showing infinite radiocarbon date were aligned using the default (top) or the recommended modified (bottom) combination of mapping parameters using the BWA aligner. High-quality hits were further filtered according to a strict (no hit on the human genome) or a best hit criterion (horse high-quality reads are discarded if showing better alternative hit on the human genome). Divergence to the modern reference genome and GC → AT misincorporation rates were calculated and reported with black and red lines as a function of base quality scores. Reads were either considered full length (0 nt) or masked for 5 nucleotides at both ends (5 nt). Further trimming (10 nucleotides) was performed and showed similar results (data not shown). BQ: Base-Quality.

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