Skip to main content

Table 8 CCRaVAT Chromosome Output File

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

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  
  1. 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.