Extended data table 3 |.
the fraction of derived alleles among putatively deaminated fragments that each of the low-coverage individuals shares with the Altai Neanderthal, Vindija 33.19, the denisovan individual and a present-day human genome
| Human (%) | Neanderthal (%) | Altai Neanderthal (%) | Vindija 33.19 (%) | Denisovan (%) | Neanderthal-Denisova (%) | Human-Neanderthal (%) | Human-Denisova (%) | |
|---|---|---|---|---|---|---|---|---|
| Les Cottés Z4–1514 | 0.67 [0.65–0.70] | 93.01 [92.89–93.13] | 18.00 [17.69–18.32] | 46.41 [46.06–46.77] | 0.86 [0.82–0.89] | 97.90 [97.83–97.98] | 97.30 [97.17–97.43] | 3.22 [3.07–3.38] |
| Goyet Q56–1 | 0.60 [0.56–0.65] | 94.38 [94.19–94.57] | 16.47 [15.93–17.02] | 53.55 [52.91–54.18] | 0.80 [0.74–0.86] | 98.17 [98.04–98.29] | 97.72 [97.49–97.92] | 2.52 [2.29–2.78] |
| Spy 94a | 0.71 [0.66–0.77] | 93.89 [93.65–94.12] | 16.52 [15.90–17.17] | 51.45 [50.70–52.21] | 0.80 [0.73–0.87] | 97.83 [97.66–97.99] | 97.62 [97.35–97.87] | 3.06 [2.75–3.39] |
| Vindija 87 | 0.36 [0.33–0.38] | 97.08 [96.97–97.19] | 6.81 [6.53–7.09] | 75.93 [75.49–76.36] | 0.37 [0.34–0.40] | 99.05 [98.98–99.12] | 98.91 [98.79–99.02] | 1.38 [1.24–1.53] |
| Mezmaiskaya 2 | 0.65 [0.62–0.69] | 92.78 [92.62–92.93] | 17.91 [17.51–18.31] | 44.65 [44.19–45.12] | 0.83 [0.79–0.88] | 97.74 [97.63–97.84] | 97.53 [97.36–97.68] | 3.38 [3.18–3.59] |
| Mezmaiskaya 1 | 0.76 [0.72–0.80] | 91.87 [91.67–92.06] | 20.30 [19.81–20.80] | 38.38 [37.85–38.91] | 0.97 [0.91–1.03] | 97.61 [97.48–97.73] | 96.80 [96.58–97.00] | 3.73 [3.49–4.00] |
| Vindija 33.16 | 3.60 [3.50–3.71] | 93.39 [93.18–93.59] | 17.09 [16.55–17.65] | 58.99 [58.36–59.63] | 3.94 [3.81–4.08] | 96.14 [95.95–96.32] | 95.46 [95.15–95.74] | 4.89 [4.56–5.24] |
| Vindija 33.25 | 3.04 [2.94–3.15] | 94.17 [93.95–94.37] | 16.69 [16.10–17.30] | 60.81 [60.11–61.49] | 3.41 [3.28–3.55] | 96.53 [96.33–96.72] | 95.79 [95.46–96.09] | 3.77 [3.46–4.12] |
| Vindija 33.26 | 3.49 [3.38–3.62] | 93.54 [93.31–93.77] | 17.04 [16.43–17.67] | 59.65 [58.94–60.36] | 3.70 [3.55–3.85] | 96.25 [96.04–96.45] | 95.40 [95.04–95.72] | 4.56 [4.21–4.95] |
| Feldhofer 1 | 4.71 [2.40–9.01] | 94.38 [87.51–97.58] | 20 [8.86–39.13] | 50.00 [34.07–65.93] | 1.80 [0.50–6.33] | 90.63 [81.02–95.63] | 96.00 [80.46–99.29] | 0 [0–12.87] |
| El Sidron 1253 | 1.29 [0.44–3.72] | 90.99 [84.21–95.03] | 17.50 [8.75–31.95] | 42.86 [30.02–56.73] | 4.35 [2.22–8.34] | 95.24 [88.39–98.13] | 97.44 [86.82–99.55] | 2.33 [0.41–12.06] |
| Denisova 4 | 2.63 [1.51–4.54] | 2.31 [1.06–4.94] | 2.13 [0.59–7.43] | 2.04 [0.56–7.14] | 71.43 [65.87–76.40] | 96.15 [91.86–98.23] | 10.00 [5.15–18.51] | 90.32 [80.45–95.49] |
| Denisova 8 | 1.60 [1.39–1.85] | 6.75 [6.13–7.43] | 1.75 [1.23–2.48] | 1.83 [1.37–2.45] | 60.02 [58.92–61.12] | 92.53 [91.66–93.32] | 15.32 [13.72–17.06] | 87.72 [86.01–89.25] |
The state of DNA fragments overlapping the positions at which the high-coverage genomes of the Altai Neanderthal, the Vindija 33.19 Neanderthal, the Denisovan individual and a present-day African (Mbuti, HGDP00982) differ from those of the great apes were investigated. Fragments longer than 35 bp with MQ ≥ 25 and within the highly mappable regions of the genome that had terminal C-to-T substitutions reported in the Supplementary Table 3.2 were used. 95% binomial confidence intervals are provided in brackets.