Table 2

List of novel and functional variants in run-of-homozygosity regions

Chromosome

Position

Reference allele

Variant allele

Variant calling/coverage

Gene

Amino acid change

PhyloP score


8

103313660

G

A

58/58

RRM2B

Pro33Ser

6.741

1

39620317

G

A

5/7*

MACF1

Arg2523Gln; Arg3025Gln

5.329

4

107449465

A

C

63/63

MGC16169

Asn34Lys

5.199

22

15980313

C

T

5/5*

LOC100287323

Val569Ile

4.997

11

64117795

G

A

4/4*

SLC22A12

Trp37Stp; Trp258Stp

4.945

10

29010439

G

C

24/24

BAMBI

Gly108Ala

4.878

20

49482400

G

A

4/4*

NFATC2

Ala778Val

4.437

1

238437608

C

T

10/12

FMN2

Pro1101Leu

3.804

1

85362528

T

-

65/69

WDR63

Splice site

3.503

3

99094433

A

G

24/34

DKFZp667G2110

Lys546Glu

3.299

3

336547

T

G

23/23

CHL1

Ser30Ala

3.014

3

46595758

C

G

27/40*

LRRC2

Arg41Gly

2.522

4

169335658

A

C

9/13*

ANXA10

Thr193Pro

2.257

5

140538797

C

T

127/127

PCDHB8

Thr333Ile

2.011


Variants with PhyloP score > 2 are listed. Asterisks indicate variants with coverage < 8× or a variant calling/coverage ratio < 0.7; the reliability of these variant calls is generally lower than that of the others.

Takata et al. Genome Biology 2011 12:R92   doi:10.1186/gb-2011-12-9-r92

Open Data