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

Table 7 CCRaVAT Permutation Summary Output File

*Gene/Window*	*Chr*	*Start*	*End*	*Case: (RV/NonRV)* *Control: (RV/NonRV)*	*Pval*	*Permutation Results*
LOC254099	1	1012320	1219359	case: (86/1213) cont: (75/581)	0.00026	Perm: 0/10 = 0
TTLL10	1	1055000	1261164	case: (164/1133) cont: (104/549)	0.047	Perm: 0/10 = 0
TNFRSF18	1	1078812	1282012	case: (164/1133) cont: (104/549)	0.047	Perm: 1/10 = 0.1
TNFRSF4	1	1086630	1289435	case: (164/1133) cont: (104/549)	0.047	Perm: 1/10 = 0.1
SDF4	1	1092212	1307334	case: (164/1133) cont: (104/549)	0.047	Perm: 0/10 = 0
B3GALT6	1	1107568	1310341	case: (164/1133) cont: (104/549)	0.047	Perm: 1/10 = 0.1
C1QDC2	1	1117751	1318766	case: (164/1133) cont: (104/549)	0.047	Perm: 0/10 = 0
UBE2J2	1	1129217	1349157	case: (164/1133) cont: (104/549)	0.047	Perm: 0/10 = 0
SCNN1D	1	1157499	1367332	case: (164/1133) cont: (104/549)	0.047	Perm: 0/10 = 0

This file provides summary statistics for all genes that achieved a p value ≤ the p value set by the -pperm command line option, which initiates permutation testing. The summary file is a tab-delimited file with 8 columns: Gene/Window name, Chromosome, Starting bp position, End bp position, Summary of the number of cases and controls that have low frequency/rare variant minor alleles, the original p value, Summary of permutations run, and Permutation p value. The output file for QuTie is the same except that column 5 contains the number of individuals with and without low frequency/rare variant minor alleles and corresponding QT values.

ISSN: 1471-2105