Extended Data Table 5. Number of alleles in selected modern humans that are present in at least one Neanderthal genome but are rare or absent in West Africans.
The analysis is based on 78,055 sites covered by at least one deaminated fragment in Oase 1. To convert the counts to estimates of ancestry, we subtract the Dinka count as an estimate of the false positive rate and divide by the number of sites covered (as indicated for the whole genome on the bottom). This gives the rate of alleles per screened site on this chromosome for this individual. We then multiply this quantity by 2%/1.32% to recalibrate the 1.32% seen genome-wide in the French to an assumed 2% genome-wide Neanderthal ancestry in the French.
| Chr | Sites | Neanderthal allele counts | Neanderthal ancestry | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Oase 1 | Ust’-Ishim | Kostenki 14 | Han | French | Dinka | Oase 1 | Ust’-Ishim | Kostenki 14 | Han | French | ||
| 1 | 6740 | 323 | 196 | 148 | 129 | 117 | 25 | 6.70% | 3.84% | 2.77% | 2.34% | 2.07% |
| 2 | 7112 | 294 | 145 | 121 | 188 | 199 | 29 | 5.65% | 2.47% | 1.96% | 3.39% | 3.62% |
| 3 | 5417 | 177 | 102 | 96 | 74 | 98 | 28 | 4.17% | 2.07% | 1.90% | 1.29% | 1.96% |
| 4 | 4495 | 359 | 86 | 63 | 141 | 96 | 42 | 10.69% | 1.48% | 0.71% | 3.34% | 1.82% |
| 5 | 4330 | 446 | 108 | 66 | 103 | 95 | 23 | 14.80% | 2.97% | 1.50% | 2.80% | 2.52% |
| 6 | 4549 | 324 | 155 | 167 | 142 | 138 | 73 | 8.36% | 2.73% | 3.13% | 2.30% | 2.16% |
| 7 | 4422 | 147 | 68 | 65 | 102 | 72 | 34 | 3.87% | 1.16% | 1.06% | 2.33% | 1.30% |
| 8 | 4322 | 131 | 132 | 72 | 35 | 38 | 14 | 4.10% | 4.14% | 2.03% | 0.74% | 0.84% |
| 9 | 3107 | 500 | 69 | 120 | 118 | 49 | 15 | 23.65% | 2.63% | 5.12% | 5.02% | 1.66% |
| 10 | 4009 | 147 | 139 | 67 | 131 | 86 | 22 | 4.72% | 4.42% | 1.70% | 4.12% | 2.42% |
| 11 | 4193 | 153 | 93 | 88 | 81 | 73 | 26 | 4.59% | 2.42% | 2.24% | 1.99% | 1.70% |
| 12 | 3456 | 456 | 160 | 54 | 125 | 93 | 10 | 19.55% | 6.58% | 1.93% | 5.04% | 3.64% |
| 13 | 2457 | 96 | 81 | 33 | 54 | 30 | 18 | 4.81% | 3.89% | 0.93% | 2.22% | 0.74% |
| 14 | 2390 | 85 | 27 | 52 | 50 | 52 | 13 | 4.56% | 0.89% | 2.47% | 2.35% | 2.47% |
| 15 | 2327 | 73 | 78 | 47 | 38 | 32 | 5 | 4.43% | 4.75% | 2.73% | 2.15% | 1.76% |
| 16 | 3139 | 90 | 121 | 68 | 43 | 39 | 8 | 3.96% | 5.45% | 2.90% | 1.69% | 1.50% |
| 17 | 2543 | 72 | 89 | 37 | 85 | 75 | 56 | 0.95% | 1.97% | −1.13% | 1.73% | 1.13% |
| 18 | 2305 | 57 | 58 | 59 | 27 | 29 | 5 | 3.42% | 3.48% | 3.55% | 1.45% | 1.58% |
| 19 | 1769 | 79 | 49 | 33 | 43 | 35 | 12 | 5.74% | 3.17% | 1.80% | 2.66% | 1.97% |
| 20 | 2492 | 107 | 29 | 62 | 56 | 43 | 12 | 5.78% | 1.03% | 3.04% | 2.68% | 1.88% |
| 21 | 1026 | 36 | 53 | 22 | 8 | 11 | 10 | 3.84% | 6.35% | 1.77% | −0.30% | 0.15% |
| 22 | 1455 | 79 | 33 | 66 | 34 | 18 | 5 | 7.71% | 2.92% | 6.35% | 3.02% | 1.35% |
|
| ||||||||||||
| All | 78055 | 4231 | 2071 | 1606 | 1807 | 1518 | 485 | 7.27% | 3.08% | 2.18% | 2.57% | “2%” |
| Subtract | Dinka | 3746 | 1586 | 1121 | 1322 | 1033 | 0 | |||||