Table 2.
Numerical description of sequenced samples. Mean coverage is calculated as the mean number of bases per position covered.
| Sample Number | Total Reads | % mtDNA Reads of Total Reads | % Unique mtDNA Reads/Total Reads | No. of unique mtDNA reads | % CR Reads/Total mtDNA Reads | % Human Genome Aligned Reads/Total Reads | % Unaligned Reads/Total Reads | Mean Strand Bias | % Coverage of Whole Mitogenome (min 2×) | % CR Coverage (min 2×) | Minimal CR Coverage | Mean CR Coverage | Mean SD of CR Coverage | Maximal CR Coverage | Minimal RL | Mean RL | SD of Mean RL | Maximal RL | Mean RL of Aligned Reads | Mean RL Other Reads | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Positive controls | |||||||||||||||||||||
| PC 1 | 1 | 102,534 | 3.11 | 1.57 | 1605 | 67.66 | 57.55 | 39.34 | 0.43 | 35.74 | 100.00 | 57 | 110.33 | 27.13 | 171 | 34 | 148.20 | 51.76 | 308 | 134.64 | 56.89 |
| PC 2 | 2 | 233,078 | 3.50 | 1.07 | 2495 | 66.33 | 56.08 | 40.42 | 0.40 | 48.96 | 100.00 | 90 | 176.01 | 41.71 | 249 | 30 | 154.69 | 54.66 | 326 | 133.98 | 51.94 |
| PC 3 | 3 | 842,114 | 2.40 | 0.40 | 3346 | 61.78 | 38.31 | 59.29 | 0.39 | 70.90 | 100.00 | 112 | 215.50 | 54.49 | 301 | 30 | 150.84 | 53.56 | 331 | 123.71 | 32.74 |
| PC 4 | 4 | 125,099 | 3.22 | 1.42 | 1777 | 66.18 | 54.03 | 42.75 | 0.40 | 34.16 | 100.00 | 60 | 114.85 | 25.00 | 168 | 33 | 135.68 | 43.69 | 311 | 122.34 | 50.64 |
| PC 5 | 5 | 197,285 | 2.89 | 1.11 | 2191 | 66.77 | 58.97 | 38.14 | 0.40 | 48.30 | 100.00 | 81 | 150.50 | 37.15 | 228 | 30 | 146.81 | 51.57 | 330 | 129.78 | 54.29 |
| PC 6 | 6 | 348,593 | 3.87 | 0.85 | 2957 | 62.09 | 63.09 | 33.04 | 0.39 | 60.70 | 100.00 | 108 | 191.57 | 43.81 | 275 | 31 | 146.26 | 47.11 | 316 | 123.06 | 64.72 |
| mean | 308,117.2 | 3.16 (0.4) | 1.07 | 2395.17 | 65.14 | 54.67 (7.83) | 42.16 (8.21) | 0.40 (0.01) | 49.79 | 100.00 | 84.67 | 159.79 (42.26) | 38.22 | 232.00 | 31.33 | 147.08 (6.39) | 50.39 | 320.33 | 127.92 | 51.87 | |
| Forensic samples | |||||||||||||||||||||
| Hair 1 | 7 | 256,877 | 88.84 | 1.39 | 3565 | 49.14 | 2.05 | 9.11 | 0.36 | 78.77 | 100.00 | 108 | 183.62 | 39.05 | 258 | 30 | 139.82 | 58.87 | 333 | 114.94 | 39.28 |
| Hair 2 | 8 | 346,147 | 65.51 | 0.24 | 819 | 44.93 | 5.58 | 28.91 | 0.42 | 54.13 | 100.00 | 2 | 26.85 | 10.28 | 49 | 32 | 112.60 | 38.72 | 241 | 119.60 | 43.63 |
| Ancient solid tissue samples | |||||||||||||||||||||
| 1 kyrs | |||||||||||||||||||||
| g52 | 9 | 7230 | 14.18 | 8.40 | 607 | 78.25 | 44.04 | 41.78 | 0.15 | 10.40 | 100.00 | 17 | 46.16 | 17.93 | 98 | 31 | 138.57 | 44.52 | 288 | 130.90 | 58.46 |
| g27 | 10 | 829,116 | 0.38 | 0.09 | 749 | 60.88 | 54.77 | 44.85 | 0.42 | 35.95 | 100.00 | 21 | 45.29 | 14.97 | 91 | 35 | 138.76 | 49.88 | 309 | 136.47 | 80.81 |
| g43 | 11 | 72,886 | 1.38 | 0.84 | 609 | 57.96 | 36.64 | 61.98 | 0.46 | 31.36 | 100.00 | 12 | 33.51 | 11.17 | 61 | 33 | 142.22 | 53.96 | 325 | 141.97 | 115.87 |
| g121 | 12 | 88,249 | 0.06 | 0.04 | 37 | 48.65 | 1.00 | 98.95 | 0.53 | 6.73 | 39.13 | 1 | 1.95 | 0.96 | 4 | 70 | 136.30 | 37.11 | 283 | 131.08 | 121.58 |
| g17 | 13 | 185,894 | 0.03 | 0.02 | 44 | 68.18 | 0.33 | 99.64 | 0.24 | 10.17 | 94.56 | 1 | 3.08 | 1.48 | 7 | 32 | 141.91 | 58.50 | 279 | 112.27 | 119.91 |
| g81 | 14 | 317,785 | 0.00 | 0.00 | 8 | 0.00 | 3.50 | 96.50 | 0.00 | 0.00 | 0.36 | 0 | 0.00 | 0.00 | 0 | 48 | 188.38 | 91.77 | 290 | 95.64 | 111.02 |
| g7 | 15 | 317,487 | 1.33 | 0.03 | 90 | 51.11 | 2.30 | 96.37 | 0.47 | 8.47 | 63.19 | 1 | 4.35 | 2.76 | 10 | 52 | 132.80 | 43.99 | 279 | 133.24 | 100.04 |
| 2 kyrs | |||||||||||||||||||||
| DT08 | 16 | 540,060 | 3.41 | 0.56 | 3048 | 56.53 | 51.42 | 45.18 | 0.39 | 71.80 | 100.00 | 59 | 171.61 | 47.51 | 253 | 31 | 142.85 | 53.37 | 311 | 130.19 | 114.19 |
| DT11-1 | 17 | 201,917 | 16.09 | 0.91 | 1829 | 53.31 | 45.88 | 38.03 | 0.40 | 68.45 | 100.00 | 37 | 96.37 | 27.00 | 145 | 31 | 142.08 | 56.34 | 315 | 138.45 | 94.66 |
| 8 kyrs | |||||||||||||||||||||
| F98E-1 | 18 | 879,757 | 0.06 | 0.01 | 69 | 55.07 | 0.03 | 99.91 | 0.52 | 8.05 | 76.29 | 1 | 2.99 | 1.60 | 8 | 37 | 96.45 | 40.30 | 342 | 104.01 | 142.54 |
| F98E-4 | 19 | 532,948 | 0.14 | 0.04 | 206 | 52.91 | 0.11 | 99.76 | 0.49 | 10.52 | 96.43 | 1 | 8.10 | 4.22 | 18 | 38 | 100.65 | 34.30 | 244 | 94.57 | 124.41 |
| F98F-2 | 20 | 534,508 | 0.84 | 0.06 | 318 | 61.32 | 0.90 | 98.26 | 0.47 | 12.36 | 99.20 | 1 | 14.42 | 6.67 | 32 | 37 | 102.75 | 37.63 | 246 | 108.52 | 128.40 |
| F98A-2 | 21 | 73 | 0.00 | 0.00 | 0 | 0.00 | 0.00 | 100.00 | 0.00 | 0.00 | 0.36 | 0 | 0.00 | 0.00 | 0 | 0 | 0.00 | 0.00 | 0 | NaN | 173.97 |
| F98B-1 | 22 | 451 | 0.22 | 0.22 | 1 | 100.00 | 0.00 | 99.78 | 1.00 | 0.00 | 0.00 | 1 | 1.00 | 0.00 | 1 | 98 | 98.00 | NA | 98 | NaN | 125.79 |
| F98C-2 | 23 | 910 | 1.21 | 0.33 | 3 | 100.00 | 0.00 | 98.79 | 0.38 | 0.88 | 12.92 | 2 | 2.70 | 0.46 | 3 | 101 | 130.33 | 25.40 | 145 | NaN | 95.68 |
| Negtive Controls | |||||||||||||||||||||
| NPC | 4146 | 0.12 | 0.12 | 5 | 20.00 | 75.01 | 24.87 | 0.00 | 0.40 | 0.00 | 1 | 1.00 | 0.00 | 1 | 76 | 152.60 | 54.00 | 226 | 151.06 | 77.85 | |
| NTC-LP | 48,396 | 0.00 | 0.00 | 0 | 0.00 | 8.41 | 91.59 | 0.00 | 0.00 | 0.36 | 0 | 0.00 | 0.00 | 0 | 0 | 0.00 | 0.00 | 0 | 162.85 | 40.23 | |
| NTC-LP | 37,769 | 0.00 | 0.00 | 1 | 100.00 | 18.35 | 81.65 | 1.00 | 0.00 | 0.00 | 1 | 1.00 | 0.00 | 1 | 135 | 135.00 | NA | 135 | 142.74 | 27.95 | |
| NTC_LP | 81,476 | 0.01 | 0.00 | 2 | 50.00 | 9.99 | 90.01 | 1.00 | 0.00 | 0.00 | 1 | 1.00 | 0.00 | 1 | 66 | 98.50 | 45.96 | 131 | 134.78 | 26.94 | |
| EX0 | 31,886 | 0.00 | 0.00 | 0 | 0.00 | 24.81 | 75.19 | 0.00 | 0.00 | 0.36 | 0 | 0.00 | 0.00 | 0 | 0 | 0.00 | 0.00 | 0 | 126.05 | 60.15 | |
| EX0 | 158,827 | 0.00 | 0.00 | 1 | 0.00 | 1.35 | 98.65 | 0.00 | 0.00 | 0.36 | 0 | 0.00 | 0.00 | 0 | 70 | 70.00 | NA | 70 | 127.15 | 42.96 | |
| mean | 60,417 | 0.02 | 0.02 | 2 | 28.33 | 22.99 | 76.99 | 0.33 | 0.07 | 0.18 | 0.50 | 0.50 | 0.00 | 0.50 | 57.83 | ||||||
SD = Standard Deviation; RL = Read Length; NPC = no primer control; PC = positive control; NTC = no template control; LP = library preparation blank; EX0 = extraction blank.