Table 8

CCRaVAT Chromosome Output File

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

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.

Lawrence et al. BMC Bioinformatics 2010 11:527   doi:10.1186/1471-2105-11-527