Table 1 Samples, methods, total number (total data) and average (down-sampled data) number of reads, and fold-enrichment (down-sampled data)
From: In-solution Y-chromosome capture-enrichment on ancient DNA libraries
Endogenous content (pre-capture) | STM1 | STM2 | PI174 | PI383 | PI435 | PI437 | ||
|---|---|---|---|---|---|---|---|---|
1.54% | 0.12% | 0.01% | 0.03% | 0.04% | 0.02% | |||
Site | Saint Martin | Saint Martin | Paso del Indio | Paso del Indio | Paso del Indio | Paso del Indio | ||
Methods | Extraction | Rohland et al., 2007 | Rohland et al., 2007 | Dabney et al., 2013 | Dabney et al., 2013 | Dabney et al., 2013 | Dabney et al., 2013 | |
Library building | Meyer and Kircher, 2010 | Meyer and Kircher, 2010 | Meyer and Kircher, 2010 | Meyer and Kircher, 2010 | Meyer and Kircher, 2010 | Meyer and Kircher, 2010 | ||
WGC | MYbaits (MYcroarray, Ann Arbor) | MYbaits (MYcroarray, Ann Arbor) | WISC (Carpenter et al., 2013) | WISC (Carpenter et al., 2013) | WISC (Carpenter et al., 2013) | WISC (Carpenter et al., 2013) | ||
YCC | YCC (this study) | YCC (this study) | YCC (this study) | YCC (this study) | YCC (this study) | YCC (this study) | ||
WGC + YCC | MYbaits + YCC | MYbaits + YCC | WISC + YCC | WISC + YCC | WISC + YCC | WISC + YCC | ||
Total data | Pre-capture | Total reads | 34,025,874 | 14,973,474 | 9,173,100 | 2,795,632 | 4,617,394 | 9,986,135 |
Mapping to chrY | 1384 | 301 | 4 | 3 | 6 | 6 | ||
On-target | 924 | 197 | 1 | 2 | 3 | 2 | ||
% of sequenced on-target | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | ||
% of chrY on-target | 67% | 65% | 25% | 67% | 50% | 33% | ||
YCC | Total reads | 68,795 | 41,884 | 159,728 | 107,796 | 41,810 | 56,157 | |
Mapping to chrY | 16,430 | 2562 | 17 | 27 | 26 | 12 | ||
On-target | 16,191 | 2541 | 17 | 27 | 25 | 12 | ||
% of sequenced on-target | 23.54% | 6.07% | 0.01% | 0.03% | 0.06% | 0.02% | ||
% of chrY on-target | 99% | 99% | 100% | 100% | 96% | 100% | ||
WGC | Total reads | 14,973,474 | 29,884,294 | 10,052,798 | 10,265,430 | 12,363,127 | 9,132,306 | |
Mapping to chrY | 6407 | 1925 | 5 | 8 | 57 | 7 | ||
On-target | 2930 | 903 | 2 | 6 | 29 | 4 | ||
% of sequenced on-target | 0.020% | 0.003% | 0.000% | 0.000% | 0.000% | 0.000% | ||
% of chrY on-target | 46% | 47% | 40% | 75% | 51% | 57% | ||
WGC + Y | Total reads | 98,540 | 30,629 | 17,212,495 | 14,557,575 | 10,181,433 | 11,356,277 | |
Mapping to chrY | 4854 | 236 | 37 | 152 | 242 | 47 | ||
On-target | 4643 | 222 | 37 | 150 | 235 | 45 | ||
% of sequenced on-target | 4.71% | 0.72% | 0.00% | 0.00% | 0.00% | 0.00% | ||
% of chrY on-target | 96% | 94% | 100% | 99% | 97% | 96% | ||
Down-sampled data | Pre-capture | Total reads | 68,795 | 30,629 | 159,728 | 107,796 | 41,810 | 56,157 |
Mapping to chrY | 2.8 | 0.2 | – | 0.2 | 0.1 | – | ||
On-target | 2.3 | 0.2 | – | – | 0.1 | – | ||
% of sequenced on-target | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | ||
% of chrY on-target | 82% | 100% | – | – | 100% | – | ||
YCC | Total reads | 68,795 | 30,629 | 159,728 | 107,796 | 41,810 | 56,157 | |
Mapping to chrY | 16,430 | 1925 | 17 | 27 | 26 | 12 | ||
On-target | 16,191.0 | 1909.8 | 17.0 | 27.0 | 25.0 | 12.0 | ||
% of sequenced on-target | 23.54% | 6.24% | 0.01% | 0.03% | 0.06% | 0.02% | ||
% of chrY on-target | 99% | 99% | 100% | 100% | 96% | 100% | ||
WGC | Total reads | 68,795 | 30,629 | 159,728 | 107,796 | 41,810 | 56,157 | |
Mapping to chrY | 38.8 | 2.7 | 0.2 | 0.1 | 0.2 | – | ||
On-target | 16.8 | 1.5 | 0.1 | 0.1 | – | – | ||
% of sequenced on-target | 0.02% | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | ||
% of chrY on-target | 43% | 56% | 50% | 100% | 0% | – | ||
WGC + Y | Total reads | 68,795 | 30,629 | 159,728 | 107,796 | 41,810 | 56,157 | |
Mapping to chrY | 4414.0 | 236.0 | 17.1 | 82.5 | 111.9 | 25.5 | ||
On-target | 4239.5 | 222.0 | 17.1 | 81.3 | 109.7 | 24.5 | ||
% of sequenced on-target | 6.16% | 0.72% | 0.01% | 0.08% | 0.26% | 0.04% | ||
% of chrY on-target | 96% | 94% | 100% | 99% | 98% | 96% | ||
Condition 1 | Condition 2 | |||||||
Fold-enrichment (down-sampled data) | YCC | Pre-capture | 7039.6 | 9549.0 | 17.0 | 27.0 | 250.0 | 12.0 |
YCC | WGC | 963.8 | 1273.2 | 170.0 | 270.0 | 25.0 | 12.0 | |
YCC | WGC + YCC | 3.8 | 8.6 | 1.0 | 0.3 | 0.2 | 0.5 | |
WGC | Pre-capture | 7.3 | 7.5 | 0.1 | 0.1 | 0.0 | 0.0 | |
WGC + YCC | Pre-capture | 1843.3 | 1110.0 | 17.1 | 81.3 | 1097.0 | 24.5 | |
WGC + YCC | WGC | 252.4 | 148.0 | 171.0 | 813.0 | 109.7 | 24.5 | |