CCRaVAT and QuTie - enabling analysis of rare variants in large-scale case control and quantitative trait association studies

Table 5 CCRaVAT Summary Output File

*Gene/Wind*	*Chr*	*Start*	*End_Pos*	*N_SNPs*	*CaseRV*	*CaseNoRV*	*ContRV*	*ContNoRV*	*ChiSq*	*P-val*	*FisherExPval*
MGC33212	3	197456409	197583455	(10/1)	2	1909	31	2903	15.5	0.000083	1.96E-05
PPIC	5	122336979	122450324	(12/6)	26	1877	7	2906	21.44	0.0000037	5.94E-06
NR3C1	5	142589325	142813087	(24/2)	8	1912	47	2869	14.71	0.00013	7.28E-05
ADAMTS2	5	178423474	178754935	(30/2)	62	1859	44	2885	16.15	0.000059	No < 30
3.8_1.5	6	29790873	29892049	(43/2)	26	1890	10	2920	16.21	0.000057	9.74E-05
KLF6	10	3761233	3867455	(14/2)	14	1907	1	2931	18.18	0.00002	2.13E-05

This file provides summary statistics for all genes that achieved a p value ≤ the p value set by the -pout command line option. The summary file is a tab-delimited file with 12 columns: Gene/Window name, Chromosome, Starting bp position, End bp position, Number of SNPs in the Gene/Window, Number of cases with low frequency/rare variant minor alleles, Number of cases without low frequency/rare variant minor alleles, Number of controls with low frequency/rare variant minor alleles, Number of controls without low frequency/rare variant minor alleles, Chi-Squared Value, Chi-Squared p value, Fisher exact p value.

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