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Table 9 QuTie Chromosome Output File

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

Gene Start End (SNPs/RV) QT+RV QT-RV QT+RV_Av QT-RV_Av RegPval BetaCoef StEr [lCI - uCI] T Ttest_Pval
MIB2 924412 1025537 (20/1) 4 597 9.014 -0.137 0.222 -9.151 7.484 [-23.819 - 5.517] 1.223 0.111
OR4G11P 938946 1039986 (25/1) 4 597 9.014 -0.137 0.222 -9.151 7.484 [-23.819 - 5.517] 1.223 0.111
MMP23B 945587 1081419 (43/6) 75 281 3.308 -0.354 0.06 -3.662 1.94 [-7.484 - 0.159] 1.884 0.03
MMP23A 983671 1097098 (46/7) 89 280 2.929 -0.493 0.059 -3.423 1.807 [-6.983 - 0.138] 1.89 0.03
CDC2L2 997120 1097869 (43/7) 89 280 2.929 -0.493 0.059 -3.423 1.807 [-6.983 - 0.138] 1.89 0.03
LOC440748 1007128 1117407 (47/8) 115 260 2.73 -0.135 0.085 -2.865 1.659 [-6.134 - 0.404] 1.724 0.04
NBPF20 1062320 1169359 (32/10) 159 224 0.713 -0.169 0.558 -0.882 1.505 [-3.847 - 2.082] 0.588 0.28
CCNL2 1105000 1211164 (35/14) 150 523 -1.291 0.224 0.281 1.515 1.403 [-1.235 - 4.266] -1.081 0.14
OR4F29 1128812 1232012 (30/17) 142 437 -1.402 0.231 0.258 1.633 1.442 [-1.193 - 4.459] -1.133 0.13
LOC440551 1136630 1239435 (30/17) 143 443 -1.407 0.204 0.262 1.611 1.435 [-1.201 - 4.423] -1.123 0.13
LOC440552 1142212 1257334 (28/15) 139 444 -1.48 0.156 0.261 1.636 1.454 [-1.214 - 4.485] -1.126 0.13
FAM87B 1157568 1260341 (22/14) 110 449 -1.612 0.209 0.254 1.822 1.596 [-1.306 - 4.949] -1.142 0.13
  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 14 columns: Gene/Window name, Starting bp position, End bp position, Number of SNPs in the Gene/Window, Number of individuals with low frequency/rare variant minor alleles, Number of individuals without low frequency/rare variant minor alleles, Mean QT value for individuals with low frequency/rare variant minor alleles, Mean QT value for individuals without low frequency/rare variant minor alleles, Linear regression p value, Beta coefficient from linear regression, Standard Error of the Beta coefficient, The lower and upper 95% Confidence Interval s of Beta, T-statistic, and T-statistic p value.