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Fig. 1 | BMC Biology

Fig. 1

From: Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences

Fig. 1

Identification and characterization of spurious and true sequence alignments. a Schematic illustration of how spurious and true sequence alignments are inferred. The human reference (hg19) is mutated to introduce changes at positions that are not known to vary among present-day humans and other hominins. True hominin sequences (blue) and spuriously aligned microbial sequences (red) are expected to show the reference, the mutated or one of the two other states with the probabilities indicated. b Frequency of all nucleotide substitutions at each position in Mezmaiskaya 1 sequence alignments. c Distributions of the proportion of mismatches in Mezmaiskaya 1 alignments. One mismatch was subtracted from all true alignments and those spurious alignments that did not carry the mutated allele. This was done to compensate for the fact that these alignments have to carry a mismatch to the mutated reference genome in order to be identified as such. d Distributions of the number of indels in Mezmaiskaya 1 alignments. See Additional file 1: Figure S1 for the distribution of mismatches and indels with the modern human and the bacterial datasets that were used as negative and positive controls, respectively

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