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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
  1. 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