Table 1.

Output summary of the novoSNP, PolyPhred, and PolyBayes SNP analysis on the SCN1A mutation and MAPT SNP data sets analyzed under different quality cutoff values

	Quality cutoff	Total number of SNPs	Correctly identified	False	positives	False	negatives
A. SCN1A
novoSNP	10	447	33	414	92.6%	0	0.0%
	15	122	32	90	73.8%	1	3.0%
	20	36	26	10	27.8%	7	21.2%
	25	26	22	4	15.4%	11	33.3%
PolyPhred	20	586	30	556	94.9%	3	9.1%
	25	510	30	480	94.1%	3	9.1%
	50	347	30	317	91.4%	3	9.1%
	75	254	30	224	88.2%	3	9.1%
	95	208	30	178	85.6%	3	9.1%
	99	189	26	163	86.2%	7	21.2%
PolyBayes	0.1	54	18	36	66.7%	15	45.5%
	0.25	46	17	29	63.0%	16	48.5%
	0.5	37	16	21	56.8%	17	51.5%
	0.75	33	16	17	51.5%	17	51.5%
B. MAPT
novoSNP	5	3424	442	2982	87.1%	10	2.2%
	10	1146	421	725	63.3%	31	6.9%
	15	484	377	107	22.1%	75	16.6%
	20	251	244	7	2.8%	208	46.0%
	25	206	203	3	1.5%	249	55.1%
PolyPhred	20	2637	280	2357	89.4%	172	38.1%
	25	2510	280	2230	88.8%	172	38.1%
	50	2243	271	1972	87.9%	181	40.0%
	75	1892	252	1640	86.7%	200	44.2%
	95	1677	207	1470	87.7%	245	54.2%
	99	1572	175	1397	88.9%	277	61.3%
PolyBayes	0.1	991	140	851	85.9%	312	69.0%
	0.25	830	136	694	83.6%	316	69.9%
	0.5	672	126	546	81.2%	326	72.1%
	0.75	567	115	452	79.7%	337	74.6%

For the SCN1A data set, the lowest novoSNP shown cutoff is 10 since all SNPs were found at this cutoff value.