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Table 7 CCRaVAT Permutation Summary Output File

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

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
  1. 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.