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

Table 8 CCRaVAT Chromosome Output File

*Gene*	*Chr*	*Start*	*Stop*	*N_SNPs*	*Case+RV*	*Case-RV*	*Cont+RV*	*Cont-RV*	*Chisq*	*PearsonPval*	*FishExPval*	*Permutations*
MIB2	1	0	107622	(5/0)	0	1924	0	2938	0	1	1
OR4G11P	1	2878	103747	(6/1)	1	1922	2	2935	0.05	0.82	1
MMP23B	1	9202	111672	(0/0)	0	1924	0	2938	0	1	1
MMP23A	1	9225	111672	(12/2)	112	1784	167	2755	0.08	0.78	No < 30
CDC2L2	1	12742	197336	(32/1)	1	1921	7	2926	2.46	0.12	0.158
LOC440748	1	39316	143660	(47/12)	380	1531	594	2329	0.14	0.71	No < 30
NBPF20	1	114476	233524	(23/1)	4	1919	2	2932	1.84	0.17	0.222
CCNL2	1	115136	226993	(13/0)	0	1924	0	2938	0	1	1
OR4F29	1	357522	544452	(7/3)	159	1756	239	2685	0.03	0.86	No < 30
LOC440551	1	519055	657573	(5/0)	0	1924	0	2938	0	1	1
LOC440552	1	558787	660167	(29/9)	207	1679	263	2640	4.74	0.029	No < 30	Perm: 1/10 = 0.1
FAM87B	1	742614	845077	(28/3)	15	1906	21	2907	0.06	0.81	0.865

This file provides summary statistics for all genes analyzed on each chromosome and is the most comprehensive output file. The summary file is a tab-delimited file with 13 columns: Gene/Window name, Chromosome, Starting bp position, End bp position, Number of SNPs in the Gene/Window and the number that are low frequency/rare, 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, and a description of any permutations run.

ISSN: 1471-2105