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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.