Table 1.

Quality trimming and mapping statistics. A number of total reads, quality filtered reads, and overall mapping rate for each replicate and each sample are described.

Sample Group	Replicate Name	Filename	Total Reads	Quality Control Reads	% Reads Passing Quality Control	Reads went into mapping	Total Reads Mapped	Overall Mapping Rate
NORM	NORM1	NORM1T_1.fastq	15,190,966	12,695,551	83.57	25,389,212	21,810,532	85.90
		NORM1T_2.fastq	15,190,966	12,695,970	83.58
	NORM2	NORM2T_1.fastq	48,392,239	48,392,019	100.00	96,783,168	93,500,856	96.61
		NORM2T_2.fastq	48,392,239	48,391,804	100.00
	NORM3	NORM3T_1.fastq	55,636,922	55,636,682	100.00	111,272,404	106,104,220	95.36
		NORM3T_2.fastq	55,636,922	55,636,437	100.00
ADH	ADH4	ADH4T_1.fastq	12,072,501	9,985,381	82.71	19,969,542	16,901,852	84.64
		ADH4T_2.fastq	12,072,501	9,985,596	82.71
	ADH5	ADH5T_1.fastq	19,656,483	16,956,030	86.26	33,910,162	29,749,778	87.73
		ADH5T_2.fastq	19,656,483	16,956,364	86.26
	ADH6	ADH6T_1.fastq	10,597,768	9,232,178	87.11	18,461,792	15,062,516	81.59
		ADH6T_2.fastq	10,597,768	9,232,503	87.12
DCIS	DCIS7	DCIS7T_1.fastq	15,265,327	12,725,074	83.36	25,447,108	20,483,162	80.49
		DCIS7T_2.fastq	15,265,327	12,725,528	83.36
	DCIS8	DCIS8T_1.fastq	21,202,092	17,943,923	84.63	35,886,362	32,592,522	90.82
		DCIS8T_2.fastq	21,202,092	17,944,297	84.63
	DCIS9	DCIS9T_1.fastq	17,680,467	15,266,076	86.34	30,530,820	27,452,402	89.92
		DCIS9T_2.fastq	17,680,467	15,266,383	86.35
CARC	CARC10	CARC10T_1.fastq	11,964,706	9,594,034	80.19	19,186,476	16,066,992	83.74
		CARC10T_2.fastq	11,964,706	9,594,135	80.19
	CARC11	CARC11T_1.fastq	12,749,664	10,291,360	80.72	20,581,584	18,862,732	91.65
		CARC11T_2.fastq	12,749,664	10,291,519	80.72
	CARC12	CARC12T_1.fastq	13,512,440	10,072,537	74.54	20,143,324	18,112,260	89.92
		CARC12T_2.fastq	13,512,440	10,072,720	74.54