Efficient linkage mapping using exome capture and extreme QTL in schistosome parasites

BMC Genomics

Table 1 Exome capture library statistics

			Female parents	Male parents	F2 untreated females	F2 treated females	F2 untreated males	F2 treated males
Total data	Number of mapped reads		87,100,659	25,711,555	21,640,228	31,561,784	39,224,999	29,417,710
Bait regions¹	Number of reads mapping to bait regions		67,492,249	11,208,843	7,037,441	15,412,158	20,936,397	15,770,592
	Percentage of reads mapping to bait regions		77.49%	43.59%	32.52%	48.83%	53.37%	53.61%
	Read depth	Mean	366	106	95	165	178	125
	Read depth	Median	274	65	82	133	159	104
Exome	Number of reads mapping to exome		65,114,964	10,837,365	6,808,470	14,939,809	20,271,770	15,311,788
	Percentage of reads mapping to exome		74.76%	42.15%	31.46%	47.33%	51.68%	52.05%
	Read depth	Mean	337	100	90	123	166	117
	Read depth	Median	250	61	78	104	150	98
Z chromosome	Comparison between Z-linked and non Z-linked regions²	Ratio of mean read depth	0.54	1.00	0.54	0.55	1.01	0.97

¹Bait regions extend beyond the exon boundaries, so the statistics for bait regions and exome are slightly different.
²The Z-linked regions are positioned between 3.5-19.5 Mb and 23.5-31 Mb on the Z chromosome.

ISSN: 1471-2164