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 |
Number of raw reads, number of merged reads, number of mapping reads before and after removing PCR duplicates, contamination estimate (Schmutzi), average depth of coverage, mitochondrial coverage, deamination pattern (Schmutzi), average fragment length and mt haplogroup (assigned with HaploGrep) are reported.