Skip to main content

Table 5 CCRaVAT Summary Output File

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

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
  1. 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.