Table 1 Summary of statistical analysis of NGS of ancient samples.
Sample identifier | HU3B | HU3G | HU4H | HU52 | HU53 | HU54 | HU55 | HU109 | HUAA |
|---|---|---|---|---|---|---|---|---|---|
Site of origin | MT | TA | MT | TA | ST | CO | CO | CO | CO |
Extraction ID | EX5 | EX3 | EX3 | EX3 | EX4 | EX3 | EX5 | EX4 | EX5 |
Total reads mapped to GRCh37 (million) | 203.1 | 278.6 | 188.7 | 164.2 | 29.0 | 33.2 | 49.2 | 116.7 | 7.1 |
Duplicate marked read pairs (million) | 3.9 | 8.2 | 3.9 | 26.2 | 0.5 | 0.4 | 0.6 | 8.7 | 1.2 |
Number of unique reads mapped to GRCh37 (million) | 195.4 | 262.1 | 180.8 | 111.8 | 28.0 | 32.3 | 48.0 | 99.4 | 4.7 |
Avg. coverage over genome (fold) | 7.02 | 9.62 | 6.52 | 4.30 | 1.04 | 1.21 | 1.76 | 3.80 | 0.17 |
Endogenous DNA content | 5.24% | 50.65% | 39.22% | 4.40% | 1.10% | 2.79% | 4.28% | 20.13% | 0.19% |
Avg. X-chromosome coverage | 3.81 | 5.36 | 3.63 | 2.32 | 0.59 | 0.66 | 0.95 | 4.01 | 0.18 |
Avg. Y-chromosome coverage | 4.33 | 5.67 | 3.09 | 2.18 | 0.44 | 0.55 | 0.80 | 0.06 | 0.00 |
Avg. mitochondrial coverage (fold) | 453 | 721 | 497 | 304 | 356 | 121 | 101 | 274 | 23 |
Mitochondrial bps covered >10-fold | 100.00% | 100.00% | 100.00% | 100.00% | 100.00% | 99.90% | 99.90% | 100.00% | 94.20% |
Number of mitochondrial bases not covered | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 19 |
Estimated mitochondrial contamination with Schmutzi | 1.00% | 1.00% | 1.00% | 1.00% | 5.00% | 1.00% | 2.00% | 1.00% | 2.00% |
Estimated X contamination with ANGSD | 1.21% | 1.01% | 0.30% | 1.83% | 11.94% | 1.30% | 1.34% | – | – |
