Additional file 1: of Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences

Table S1. Summary of bacterial sequences. Table S2. Summary of S. cerevisiae sequences. Table S3. Summary of A. laibachii sequences. Table S4. Percentage of sequences with a given number of mismatches for each type of alignments. Table S5. Sequence length cutoffs in hominin ancient DNA studies [39–65]. Table S6. Modern human contamination. Figure S1. Characteristics of spurious and true alignments. Figure S2. Length distribution of mapped sequences. Figure S3. Proportion of spurious alignments by sequence length for SH samples. Figure S4. Spurious alignments in SH samples and the effect of different filters. Figure S5. Significance of Neandertal-lineage assignment for different minimum length cutoffs. Figure S6. Lineage assignment as a function of sequence length. (PDF 767 kb)