ExCNVSS: A Noise-Robust Method for Copy Number Variation Detection in Whole Exome Sequencing Data

Table 3

CNV detection performances using 10 real data sets. A different germline sample (NA19152) was used as a control data set.

sample ID	ExCNVSS		ExCNVSS_noRatio		Excavator		Contra		ExomeCNV
	Correctly detected instances (gain/loss)	FNR/FPR; (%)	Correctly detected instances (gain/loss)	FNR/FPR; (%)	Correctly detected instances (gain/loss)	FNR/FPR; (%)	Correctly detected instances (gain/loss)	FNR/FPR; (%)	Correctly detected instances (gain/loss)	FNR/FPR; (%)
NA12843	31	77.04/	63	53.33/	47	65.19/	11	91.85/	64	52.59/
	(3/28)	12.04	(27/36)	14.99	(0/47)	6.20	(0/11)	0.36	(17/47)	80.09
NA12842	12	88.57/	39	62.86/	1	99.05/	3	97.14/	28	73.33/
	(3/9)	11.43	(25/14)	17.03	(0/1)	4.93	(0/3)	0.32	(17/11)	56.75
NA12748	18	82.18/	36	64.36/	1	99.01/	1	99.01/	32	68.32/
	(4/14)	11.25	(24/12)	14.47	(0/1)	6.00	(0/1)	0.26	(15/17)	70.67
NA12718	50	57.26/	76	35.04/	47	59.83/	17	85.47/	13	88.89/
	(6/44)	8.37	(31/45)	14.08	(0/47)	2.42	(0/17)	0.34	(0/13)	3.50
NA12275	22	77.55/	43	56.12/	5	94.90/	2	97.96/	9	90.82/
	(9/13)	12.13	(33/10)	13.74	(0/5)	2.70	(1/1)	0.31	(0/9)	1.85
NA12273	32	71.68/	40	64.60/	11	90.27/	17	84.96/	2	98.23/
	(0/32)	11.68	(27/13)	15.12	(0/11)	2.95	(0/17)	0.38	(0/2)	2.60
NA12272	35	64.65/	42	57.58/	16	83.84/	1	98.99/	18	81.82/
	(6/29)	12.58	(31/11)	13.86	(5/11)	2.36	(0/1)	0.18	(5/13)	1.43
NA11843	19	81.19/	37	63.37/	12	88.12/	1	99.01/	34	66.34/
	(10/9)	9.74	(26/11)	15.86	(0/12)	6.62	(0/1)	0.20	(19/15)	78.30
NA10847	13	86.32/	37	61.05/	7	92.63/	7	92.63/	9	90.53/
	(10/3)	9.58	(36/1)	16.24	(7/0)	2.56	(4/3)	0.35	(7/2)	2.03
NA06984	25	77.68/	46	58.93/	15	86.61/	13	88.39/	44	60.71/
	(2/23)	11.75	(32/14)	14.36	(0/15)	5.86	(0/13)	0.22	(15/29)	72.78