Skip to main content

Table 6 QuTie Summary Output File

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

Gene

Chr

Start

End_pos

SNPs/rvSNPs

QT+RV

QT-RV

QT+RV mean

QT-RV mean

p-val

BetaCoef

St.Er

[lowCI - upCI]

t-test

t-test_p-val

MIB2

1

0

107622

(10/1)

106

1125

-0.367

0.037

6.77E-05

0.404

0.101

[0.206 - 0.602]

-3.975

3.72E-05

GOLGA8C

15

18977714

19091040

(29/4)

127

1097

-0.347

0.042

3.19E-05

0.389

0.093

[0.206 - 0.571]

-4.149

1.78E-05

TPO

2

1346242

1575502

(29/6)

70

1158

0.478

-0.028

4.00E-05

-0.506

0.122

[-0.746 - -0.266]

4.107

1.80E-05

EXOC3

5

446375

570407

(24/1)

4

1228

1.935

-0.006

1.00E-04

-1.941

0.498

[-2.918 - -0.964]

3.874

5.12E-05

C10orf110

10

1008606

1130138

(66/4)

111

1116

0.379

-0.036

4.00E-05

-0.415

0.099

[-0.609 - -0.221]

4.161

1.48E-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 15 columns: Gene/Window name, Chromosome, 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, The mean QT value of individuals with low frequency/rare variant minor alleles, The mean QT value of individuals without low frequency/rare variant minor alleles, The p value of the linear regression, The Beta coefficient from the linear regression, The Standard Error of the Beta Coefficient, the lower and upper 95% confidence intervals of Beta, The t-statistic, and The t-statistic p value.