Table 1. Comparison of read-mapping between enriched and unenriched libraries.

We report the average number of read pairs after quality trimming, the number of read pairs that properly mapped to the full genome, and the percent of the reads which mapped to the full genome. The standard deviations are given in parentheses. Also included are the number of read pairs that mapped to the target bait regions, the percentage of the properly paired reads that mapped to the target regions, and the percentage of the target bait regions with a coverage of three or more reads (≥3×). For individual sample statistics see S3 Table.

	Post-trimming Read Pairs	Properly Paired Reads Mapped to the Full Genome	% all reads mapped	Properly Paired Mapped Reads (Target Regions)	% Properly paired reads mapped to target regions	% of target regions with coverage ≥3x
Enriched Datasets (n = 36)	2,504,426 (1,289,201)	2,036,689 (1,198,782)	79.8% (11.8%)	274,708 (146,076)	13.82% (2.27%)	52.6% (14.27%)
Unenriched Datasets (n = 5)	3,000,000 (0*)	2,439,858 (88,964)	81.3% (3.0%)	18,562 (872)	0.76%. (0.01%)	10.65% (1.19%)

^*For each unenriched dataset, the number of reads used was down sampled to three million after read trimming and quality filtering. See text for more details.