Table 2. Sequencing reads obtained from KIT locus captures mapped against the mouse genome (mm9).

Sequences were also mapped against hg18 as a quality control measure. Total number of reads sequenced and the number and percentage of these reads that mapped uniquely to the mouse genome are shown for each sample (A). Each of the samples contained numerous reads that mapped to hg18, which indicated a small degree of contaminate from human DNA. Despite this contamination from human DNA, a > 70× median coverage of the primary target region was achieved in 5 of 5 samples, with a maximum median coverage of 215× observed in sample W-40J (B). The BALB/c (msgDNA + control) reads were obtained by pooling 3 regions of a 16 channel PTP run.

A.	mouse (mm9)
Sample	Reads	Unique	(%)
W-39J	188.823	153.646	81%
W-41J	485.377	300.278	62%
W-73J	474.377	235.795	50%
W-40J	371.694	280.109	75%
W-20J	540.095	244.870	45%
msgDNA	29.422	22.284	76%
B.	Coverage
Sample	Target Covered	Reads	(%)	Coverage (median)	#Contigs	Fold Enrichment*
W-39J	98.40%	105.354	68.60%	146	18	10077
W-41J	97.80%	109.140	36.30%	128	22	5332
W-73J	97.80%	62.829	26.60%	74	23	3907
W-40J	97.80%	168.841	45.40%	215	15	6669
W-20J	94.80%	65.014	26.60%	78	22	3907
msgDNA	99.70%	16.711	75.00%	18	N/A	11017

^*Fold enrichment was calculated as (% reads on target) / (Kit interval size in bases / mm9 genome size in bases), where kit interval size = 183,806 bases, and mm9 genome size = 2,700 Mb.