A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage

BMC Bioinformatics

Table 1 Results by PolyFreq and PolyBayes on eighteen data sets of EST sequences

Data set	Size	PolyBayes (trimmed)				PolyFreq (full length)				PolyBayes (full length)
		TP	FP	FN	NSU	TP	FP	FN	NSU	TP	FP	FN	NSU
Hs.119589	4403	12	170	50	1491	5	24	57	4391	12	152	50	1531
Hs.129673	1665	7	48	11	1457	5	11	13	1662	T/A
Hs.148340	1603	3	36	9	1563	4	9	8	1583	3	67	9	1560
Hs.170622	1514	1	37	12	429	3	18	10	1507	2	73	11	365
Hs.178551	1685	5	62	12	1632	6	14	11	1676	T/A
Hs.180909	1017	3	50	6	983	3	20	6	1012	3	164	6	996
Hs.187199	2041	T/A					N/A		1997	T/A
Hs.198281	3156	9	110	22	3077	15	54	16	3149	T/A
Hs.350927	1017	5	42	11	976	9	21	7	1015	6	139	10	995
Hs.356331	1441	2	55	9	318	1	14	10	1436	2	85	9	239
Hs.356572	2822	0	46	2	2534	0	17	2	2821	T/A
Hs.439552	7163	T/A					N/A		6873	T/A
Hs.444467	4033		N/A		805		N/A		4028		N/A		679
Hs.446628	1490	4	32	12	1338	5	12	11	1486	T/A
Hs.520640	4120	T/A				9	52	27	4099	T/A
Hs.522463	8294	T/A					N/A		8280	T/A
Hs.524390	4462	T/A				9	48	24	4454	T/A
Hs.544577	7537	14	60	43	1716	10	17	47	7517	18	175	39	1556

The mark N/A means that no SNP from dbSNP was mapped to the anchor sequence because of lack of a RefSeq sequence. The mark T/A means that PolyBayes terminated abnormally without producing any output file. A candidate SNP from the program is considered as true positive (TP) if it is in dbSNP or false positive (FP) otherwise. A SNP from dbSNP that occurs in the data set is considered as false negative (FN) if it is not reported as a candidate SNP from the program. The number of sequences used (NSU) by the program in generation of candidate SNPs is reported.

ISSN: 1471-2105