SNVHMM: predicting single nucleotide variants from next generation sequencing

BMC Bioinformatics

Table 2 Comparison of statistical performance of SNVHMM with SNVMix2 with different mapping quality (MQ) and base quality (BQ) threshold for 40X data

Model	MQ	BQ	TP	FP	TN	FN	Sensitivity(%)	Specificity(%)	Accuracy(%)	F-score
SNVHMM	50	20	281	77	115	24	92.13	59.89	79.68(MVC = 7)	0.8477
	40	20	283	83	109	22	92.78	56.77	78.87(MVC = 6)	0.8435
	30	20	273	77	115	32	89.51	59.89	78.07(MVC = 9)	0.8336
	30	10	289	79	113	16	94.75	58.85	80.88(MVC = 9)	0.8588
	20	10	279	86	106	26	91.47	55.21	77.46(MVC = 8)	0.8328
	10	5	281	87	105	24	92.13	54.69	77.67(MVC = 7)	0.8351
SNVMix2_TI	50	20	291	109	83	14	95.40	43.23	75.25	0.8255
	40	20	294	113	79	11	96.39	41.14	75.05	0.8258
	30	20	294	115	77	11	96.39	40.10	74.65	0.8235
	30	10	295	113	79	10	96.72	41.15	75.25	0.8275
	20	10	294	117	75	11	96.39	39.06	74.25	0.8212
	10	5	295	118	74	10	96.72	38.54	74.25	0.8217
SNVMix2_TO	50	20	283	86	106	22	92.79	55.21	78.27	0.8398
	40	20	287	93	99	18	94.10	51.56	77.67	0.8380
	30	20	287	96	96	18	94.10	50.00	77.06	0.8343
	30	10	284	105	87	21	93.11	45.31	74.65	0.8184
	20	10	291	105	87	14	95.40	45.31	76.06	0.8302
	10	5	291	104	88	14	95.41	45.83	76.26	0.8314

ISSN: 1471-2105