Table 1.
Samples, methods, total number (total data) and average (down-sampled data) number of reads, and fold-enrichment (down-sampled data)
| 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 | |
Ten replicates per library were obtained by down-sampling to the minimum number of retained reads within each sample (underlined in “Total data” rows). The “Mapping to chrY” section indicates the number of unique reads mapping to the Y-chromosome. “On-target” refers to the unique on-target reads. “%of sequenced on-target” and “% of chrY on-target” refer to the percentage of on-target reads with respect to the total sequenced reads and to the total reads mapping to the Y-chromosome, respectively. The fold-enrichments were calculated with the down-sampled data, by dividing the number of on-target reads in Condition 1 by the number of on-target reads in Condition 2; when the denominator was 0, we assigned the number of on-target reads in Condition 1