Table 2 Sequencing and mapping summary.
Sample ID | Raw reads | Merged reads (%) | Mapped reads prior rmdup | Mapped reads after rmdup | Contamination estimate | mtDNA Average Coverage Depth | mtDNA Average Coverage (%) | Deamination pattern | Average fragment length (bp) | Hg | ||
---|---|---|---|---|---|---|---|---|---|---|---|---|
First iteration (%) [low-high] | Final iteration (%) [low-high] | 5′ (%) | 3′ (%) | |||||||||
SM 4 | 1042513 | 975974 (93.62) | 14659 | 10820 | 0 [0–0.05] | 2 [1–3] | 35.73 | 98.36 | 41.19 | 40.68 | 54.7 | J1c |
SM 8.1 | 291072 | 280395 (93.33) | 17037 | 11026 | 0 [0–1.5] | 1 [0–2] | 31.01 | 98.05 | 46.00 | 49.32 | 46.6 | U5a1a2b |
SM 24.2 | 138644 | 133841 (96.54) | 8598 | 7666 | 0 [0–0.5] | 1 [0–2] | 20.92 | 97.63 | 35.90 | 35.90 | 45.2 | HV1a’b’c |
GM 30.3 | 140659 | 133681 (95.04) | 4692 | 4194 | 5 [2–8] | 2 [1–3] | 13.61 | 95.38 | 42.46 | 41.33 | 53.8 | K1c1 |
BM AG | 252894 | 242542 (95.91) | 67931 | 52866 | 0 [0–0.5] | 1 [0–2] | 178.75 | 100 | 21.10 | 21.00 | 56.0 | U5b2a1a1 |
BM 2 | 1129167 | 1072135 (94.95) | 568403 | 362803 | 4.5 [4–5] | 2 [1–3] | 1299.92 | 100 | 20.00 | 20.00 | 59.4 | N1b1a1 |
BM 3 | 455909 | 398419 (87.39) | 125888 | 76387 | 0 [0–1] | 2 [1–3] | 310.93 | 100 | 23.33 | 22.51 | 67.4 | H3ak |
BM 5 | 241044 | 223147 (92.58) | 44418 | 39517 | 6.5 [5.5–7.5] | 1 [0–2] | 155.55 | 100 | 25.95 | 24.28 | 65.2 | H5a1a |
BM 6 | 795728 | 767050 (96.40) | 272955 | 170311 | 0 [0–1] | 1 [0–2] | 557.29 | 100 | 32.25 | 30.10 | 54.2 | H7a1a |
BM 9 | 306514 | 293319 (95.70) | 38873 | 27053 | 0 [0–0.05] | 1 [0–2] | 102.67 | 99.96 | 32.74 | 31.10 | 62.6 | H7 |
BM 10 | 1051289 | 1015983 (96.64) | 190927 | 120090 | 8 [9–7] | 1 [0–2] | 411.12 | 100 | 24.67 | 23.51 | 56.7 | U4c2a |
BM 15 | 308266 | 292881 (95.01) | 67093 | 43783 | 0 [0–0.05] | 1 [0–2] | 170.28 | 100 | 28.55 | 26.10 | 64.4 | T2b |
BM 24 | 336874 | 306128 (90.87) | 48355 | 39312 | 5.5 [4.5–6.4] | 1 [0–2] | 136.90 | 99.98 | 31.07 | 27.00 | 57.5 | I2 |
BM 31 | 291132 | 259451 (89.12) | 35740 | 31783 | 57 [56–58] | 16 [15–17] | 122.07 | 97.04 | 29.24 | 26.46 | 63.6 | J1c9 |
BM 36 | 542629 | 521894 (96.18) | 244787 | 178811 | 0 [0–0.1] | 1 [0–2] | 599.48 | 100 | 33.24 | 31.47 | 55.6 | N1 |
BM 40 | 199895 | 190493 (95.30) | 45850 | 40103 | 0 [0–0.05] | 2 [1–3] | 130.67 | 99.97 | 28.72 | 29.12 | 54.0 | T2e2a |
BM 44 | 167444 | 162418 (97.00) | 40293 | 32973 | 0 [0–0.05] | 2 [1–3] | 100.58 | 99.93 | 34.99 | 33.01 | 50.5 | HV0 |
BM 51A | 1025635 | 971945 (94.77) | 27811 | 289429 | 46.5 [45.5–47.5] | 10 [9–11] | 84.19 | 99.06 | 35.98 | 31.63 | 56.9 | K1c1 |
BM 58A | 164453 | 156982 (95.46) | 39604 | 33144 | 0 [0–0.05] | 2 [1–3] | 113.77 | 99.97 | 30.82 | 28.72 | 56.9 | K1c1 |
BM 59A | 319622 | 303936 (95.09) | 95874 | 77103 | 0 [0–0.05] | 2 [1–3] | 258.96 | 100 | 30.16 | 29.86 | 55.6 | T2b |
BM 61 | 240732 | 230927 (95.93) | 63892 | 56475 | 7 [6–8] | 1 [0–2] | 186.98 | 99.97 | 29.29 | 28.74 | 54.9 | J1c6 |
BM 68 | 518653 | 503547 (97.09) | 174125 | 126713 | 5 [2–8] | 3 [4–2] | 400.39 | 99.98 | 33.31 | 32.98 | 52.4 | K1c1 |
BM 69 | 361277 | 343403 (95.05) | 70252 | 55118 | 0 [0–0.05] | 1 [0–2] | 165.64 | 100 | 32.95 | 30.15 | 49.8 | H5b |
BM 73 | 311752 | 292048 (93.68) | 127325 | 95877 | 0 [0–0.05] | 1 [0–2] | 256.74 | 100 | 37.23 | 35.02 | 44.4 | H76a |
BM 76 | 486546 | 473556 (97.33) | 86904 | 61483 | 0 [0–0.05] | 1 [0–2] | 192.58 | 100 | 22.55 | 23.35 | 51.9 | H4a1 |