| Autor: |
Peyrégne, Stéphane, Peter, Benjamin M. |
| Rok vydání: |
2020 |
| DOI: |
10.6084/m9.figshare.12960516 |
| Popis: |
Additional file 1: Supplementary Figures, Notes and Tables. Figure S1: Contamination estimates on simulated datasets with different GC contents (A) and average sequence lengths (B). Figure S2: Effect of different rates of errors (including polymorphisms) between the endogenous and contaminating sequences. Figure S3: Contamination estimates on artifical mixtures of Neandertal and 1 to 10% (in steps of 1%) present-day human DNA sequences. Figure S4: Contamination estimates for ancient DNA datasets generated from domesticated species. Figure S5: Comparison of AuthentiCT, PMDtools and simple filters (based on the observed number of C-to-T substitutions) to identify ancient DNA sequences. Figure S6: Comparison of AuthentiCT and PMDtools to classify ancient and present-day DNA sequences for multiple datasets (when false positive rates are below 0.03). Figure S7: Comparison of the distributions of likelihood ratios («Score») computed with AuthentiCT (solid lines) and PMDtools (dashed lines) for different mixtures of ancient and present-day DNA sequences. Figure S8: Example of a Denisovan sample (Denisova 2, [5]) with a likely deaminated contaminant and the associated contamination underestimate from AuthentiCT. Figure S9: Runtime (wall clock) to estimate contamination depending on the number of sequences. Figure S10: Runtime (wall clock) to estimate contamination depending on the number of sequences when the model parameters values are provided in a configuration file (e.g. fitted a priori with a subset of the sequences). Table S1: Contamination estimates in the Neandertal datasets used in Figure 3. Table S2: Summary of the libraries used to compare the contamination estimates from AuthentiCT and a method based on the proportion of shared derived alleles with a present-day human genome («Ancestry-based» estimates). Supplementary Note 1: Excess of adjacent C-to-T substitutions inside ancient DNA sequences. Supplementary Note 2: Inference of the structure of ancient DNA fragments. Supplementary Note 3: Differences in contamination estimates per sequence and per base. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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