Table 5. Variant detection from independent library preparations.

					Run 1		Run 2		Run 3
Sample	Gene	Exon/ Intron	c. Name	p. Name	Frequency (%) | Quality	Total Coverage | Normalized Coverage	Frequency (%) | Quality	Total Coverage | Normalized Coverage	Frequency (%) | Quality	Total Coverage | Normalized Coverage
NA13707	BRCA1	Exon10	c.1175_1214del40	p.Leu392GlnfsTer5	46.9 | 37	1459 | 0.43	49.7 | 37	2150 | 0.79	54.0 | 37	1589 | 0.63
			c.2082C>T		53.9 | 37	1156 | 0.32	48.0 | 37	2206 | 0.75	49.5 | 37	1163 | 0.43
			c.2311T>C		50.5 | 38	1015 | 0.28	45.4 | 38	1458 | 0.50	46.5 | 38	923 | 0.34
			c.2315T>C	p.Val772Ala	50.2 | 37	988 | 0.28	54.6 | 37	1419 | 0.50	53.8 | 38	900 | 0.34
			c.2612C>T	p.Pro871Leu	50.8 | 38	1256 | 0.35	50.3 | 38	1652 | 0.58	51.9 | 38	1160 | 0.44
			c.3113A>G	p.Glu1038Gly	50.2 | 38	835 | 0.23	49.3 | 38	1205 | 0.42	50.4 | 38	857 | 0.33
			c.3548A>G	p.Lys1183Arg	48.1 | 37	1537 | 0.42	47.3 | 37	1587 | 0.55	50.2 | 37	1322 | 0.50
		Exon12	c.4308T>C		50.5 | 38	9011 | 2.47	50.1 | 38	2727 | 0.93	50.1 | 38	4408 | 1.64
		Exon15	c.4837A>G	p.Ser1613Gly	50.5 | 38	3946 | 1.09	48.7 | 38	2779 | 0.96	48.9 | 38	2738 | 1.05
	BRCA2	Exon10	c.1114A>C	p.Asn372His	50.0 | 38	1174 | 0.32	48.9 | 38	1457 | 0.49	47.4 | 38	1166 | 0.43
		Exon11	c.3396A>G		50.3 | 38	1032 | 0.28	52.5 | 38	1348 | 0.46	47.8 | 38	938 | 0.35
			c.4563A>G		100 | 37	1064 | 0.29	99.9 | 37	1552 | 0.52	99.9 | 37	935 | 0.35
			c.6513G>C		98.0 | 33	1327 | 0.36	100 | 37	1407 | 0.47	99.8 | 36	993 | 0.36
		Exon14	c.7397T>C	p.Val2466Ala	99.8 | 35	3086 | 0.83	99.7 | 34	2456 | 0.83	99.7 | 35	2425 | 0.89
NA14634	BRCA1	Exon10	c.4065_4068delTCAA	p.Asn1355LysfsTer10	49.8 | 34	1531 | 0.38	49.1 | 34	1903 | 0.70	48.9 | 36	2093 | 0.60
	BRCA2	Exon11	c.3396A>G		51.0 | 38	1201 | 0.30	51.0 | 38	1306 | 0.48	51.8 | 38	1497 | 0.44
			c.4563A>G		99.9 | 37	1302 | 0.33	100 | 37	1540 | 0.57	100 | 37	1645 | 0.48
			c.5744C>T	p.Thr1915Met	52.3 | 36	968 | 0.28	48.1 | 36	950 | 0.42	52.6 | 37	1177 | 0.38
			c.6513G>C		98.2 | 33	1404 | 0.35	100 | 37	1332 | 0.48	99.9 | 36	1413 | 0.41
		Exon14	c.7242A>G		49.0 | 37	3248 | 0.82	48.0 | 37	2279 | 0.85	48.5 | 37	2940 | 0.86
			c.7397T>C	p.Val2466Ala	99.6 | 35	3292 | 0.82	99.3 | 33	2293 | 0.85	99.7 | 36	2969 | 0.86
		Intron 16	c.7806-14T>C		99.9 | 38	4932 | 1.29	99.9 | 38	4076 | 1.61	99.8 | 38	5049 | 1.54
Clin-1	BRCA2	Exon9	c.755_758delACAG	p.Asp252ValfsTer24	51.6 | 34	8396 | 2.04	52.6 | 35	1296 | 1.12	49.3 | 35	4685 | 1.59
		Exon10	c.1114A>C	p.Asn372His	99.8 | 38	1211 | 0.30	100 | 38	565 | 0.50	99.9 | 38	1385 | 0.47
		Exon11	c.4563A>G		99.9 | 37	1736 | 0.42	100 | 37	667 | 0.59	99.9 | 37	1397 | 0.47
			c.6513G>C		97.4 | 32	1429 | 0.34	100 | 37	540 | 0.46	99.9 | 35	1346 | 0.45
		Exon14	c.7397T>C	p.Val2466Ala	99.6 | 35	3186 | 0.78	99.9 | 34	887 | 0.77	99.8 | 36	2532 | 0.86
		Intron 16	c.7806-14T>C		48.1 | 38	4745 | 1.20	50.2 | 38	1622 | 1.45	49.8 | 38	4024 | 1.40

Three samples with previously confirmed variants had libraries prepared independently three times. The variants in the three samples were detected in all runs (NGS sample statistics in S5 Table).