Extended Data Table 7. Sequencing metrics on all five libraries for each of four capture probe panels.
| Library | Panel | No. target SNPs | Fragments going into alignment | Fragments mapped to genome | Fragments on target after dup. removal and MAPQ37 filter | % SNPs hit at least once | Average coverage on SNPs |
|---|---|---|---|---|---|---|---|
| A9032 | 390k | 393,577 | 10,849,144 | 2,235,955 | 133,564 | 26.5% | 0.34 |
| A9033 | 390k | 393,577 | 17,159,085 | 2,808,704 | 73,824 | 15.9% | 0.19 |
| A9034 | 390k | 393,577 | 16,902,935 | 3,256,438 | 142,520 | 27.7% | 0.36 |
| A5227 | 390k | 393,577 | 63,441,719 | 22,124,247 | 195,161 | 36.0% | 0.5 |
| A5252 | 390k | 393,577 | 60,181,844 | 14,278,978 | 180,626 | 33.3% | 0.46 |
| All 5 | 390k | 393,577 | 168,534,727 | 44,704,322 | 724,653 | 73.0% | 1.84 |
|
| |||||||
| A9032 | 840k | 842,630 | 25,105,625 | 3,801,435 | 178,015 | 17.6% | 0.21 |
| A9033 | 840k | 842,630 | 29,196,969 | 4,655,434 | 183,093 | 17.9% | 0.22 |
| A9034 | 840k | 842,630 | 35,780,652 | 5,968,851 | 200,767 | 19.3% | 0.24 |
| A5227 | 840k | 842,630 | 28,209,496 | 4,276,439 | 152,411 | 15.3% | 0.18 |
| A5252 | 840k | 842,630 | 20,286,540 | 1,630,343 | 106,943 | 11.2% | 0.13 |
| All 5 | 840k | 842,630 | 138,579,282 | 20,332,502 | 818,648 | 51.7% | 0.97 |
|
| |||||||
| A9032 | 1000k | 997,780 | 26,088,835 | 2,964,094 | 159,162 | 13.5% | 0.16 |
| A9033 | 1000k | 997,780 | 26,641,358 | 4,490,372 | 158,614 | 13.3% | 0.16 |
| A9034 | 1000k | 997,780 | 28,795,043 | 4,985,140 | 154,177 | 13.0% | 0.15 |
| A5227 | 1000k | 997,780 | 25,848,311 | 4,395,413 | 71,537 | 6.4% | 0.07 |
| A5252 | 1000k | 997,780 | 25,691,323 | 2,254,636 | 53,932 | 5.0% | 0.05 |
| All 5 | 1000k | 997,780 | 133,064,870 | 19,089,655 | 596,107 | 36.1% | 0.6 |
|
| |||||||
| A9032 | Archaic | 1,749,385 | 19,329,832 | 2,086,208 | 205,095 | 10.0% | 0.12 |
| A9033 | Archaic | 1,749,385 | 24,629,023 | 2,768,355 | 237,818 | 11.4% | 0.14 |
| A9034 | Archaic | 1,749,385 | 31,200,466 | 3,783,805 | 257,351 | 12.2% | 0.15 |
| A5227 | Archaic | 1,749,385 | 27,659,125 | 3,606,375 | 195,356 | 9.6% | 0.11 |
| A5252 | Archaic | 1,749,385 | 31,472,143 | 2,435,080 | 136,637 | 6.8% | 0.08 |
| All 5 | Archaic | 1,749,385 | 134,290,589 | 14,679,823 | 1,022,046 | 34.6% | 0.58 |
|
| |||||||
| A9032 | Combined | 3,801,245 | 81,373,436 | 11,087,692 | 719,146 | 15.5% | 0.19 |
| A9033 | Combined | 3,801,245 | 97,626,435 | 14,722,865 | 698,890 | 15.1% | 0.18 |
| A9034 | Combined | 3,801,245 | 112,679,096 | 17,994,234 | 806,589 | 17.0% | 0.21 |
| A5227 | Combined | 3,801,245 | 145,158,651 | 34,402,474 | 666,195 | 14.2% | 0.18 |
| A5252 | Combined | 3,801,245 | 137,631,850 | 20,599,037 | 531,873 | 11.4% | 0.14 |
| All 5 | Combined | 3,801,245 | 574,469,468 | 98,806,302 | 3,406,685 | 45.5% | 0.90 |