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Table 2 The 156 reliable marker SNPs that induced amino acid changes showing ≥10 read depths

From: Genome resequencing and bioinformatic analysis of SNP containing candidate genes in the autoimmune vitiligo Smyth line chicken model

Contig ID

c

Ref Pos

Ref base

Called base

Impact

SNP%

Gene symbol

DNA change

AA Change

Depth

A Cnt

C Cnt

G Cnt

T Cnt

Del

NC_006088

1

12587537

C

T

N-Syn

0.80

FGL2

c.368C > T

T123I

10

0

-

0

8

0

NC_006088

1

24296415

G

C

N-Syn

1.00

CTTNBP2

c.2600G > C

R867P

12

0

12

-

0

0

NC_006088

1

33755434

G

A

N-Syn

0.91

TBC1D30

c.304G > A

V102I

11

10

0

-

0

0

NC_006088

1

34386453

G

A

N-Syn

1.00

HELB

c.2342G > A

G781E

12

12

0

-

0

0

NC_006088

1

34386455

C

T

N-Syn

1.00

HELB

c.2344C > T

R782W

12

0

-

0

12

0

NC_006088

1

45803846

A

G

N-Syn

1.00

LOC417921

c.1457A > G

Q486R

11

-

0

11

0

0

NC_006088

1

45804772

T

A

N-Syn

0.92

LOC417921

c.1700 T > A

I567K

13

12

1

0

-

0

NC_006088

1

54936701

G

T

N-Syn

0.80

STAB2

c.6155G > T

A2052D

10

0

0

-

8

0

NC_006088

1

67320079

C

C|A

N-Syn

0.77

CASC1

c.[949C > C] + [949C > A]

V317V, V317F

13

10

-

0

0

0

NC_006088

1

82856208

G

T

N-Syn

1.00

CD200R1

c.197G > T

R66L

11

0

0

-

11

0

NC_006088

1

88049869

C

T

N-Syn

0.90

LOC418423

c.229C > T

V77I

10

0

-

0

9

0

NC_006088

1

88157238

C

T

N-Syn

1.00

CGGBP1

c.428C > T

R143Q

10

0

-

0

10

0

NC_006088

1

105941417

T

C

N-Syn

0.90

SETD4

c.1186 T > C

I396V

10

0

9

0

-

0

NC_006088

1

107377588

C

G

N-Syn

0.92

LCA5L

c.1331C > G

G444A

13

0

-

12

0

0

NC_006088

1

108406755

T

T|C

N-Syn

0.77

LOC770616

c.[37 T > T] + [37 T > C]

M13M, M13V

13

0

10

0

-

0

NC_006088

1

108764081

C

T

N-Syn

0.91

UBASH3A

c.1144C > T

L382F

11

0

-

0

10

0

NC_006088

1

109036880

G

T

N-Syn

1.00

CBS

c.1492G > T

Q498K

10

0

0

-

10

0

NC_006088

1

112264749

A

G

N-Syn

1.00

OTC

c.5A > G

L2P

12

-

0

12

0

0

NC_006088

1

112303781

A

G

N-Syn

1.00

RPGR

c.2359A > G

I787V

13

-

0

13

0

0

NC_006088

1

112303950

G

A

N-Syn

1.00

RPGR

c.2528G > A

G843E

10

10

0

-

0

0

NC_006088

1

121737171

G

A

N-Syn

1.00

FANCB

c.1988G > A

R663K

12

12

0

-

0

0

NC_006088

1

121737188

C

A

N-Syn

1.00

FANCB

c.2005C > A

L669M

12

12

-

0

0

0

NC_006088

1

133392696

A

G

N-Syn

1.00

MFSD9

c.790A > G

F264L

11

-

0

11

0

0

NC_006088

1

137555484

C

T|C

N-Syn

0.79

MYO16

c.[1232C > T] + [1232C > C]

T411T, T411I

14

0

-

0

11

0

NC_006088

1

138584430

C

T

N-Syn

0.90

ANKRD10

c.551C > T

R184H

10

0

-

0

9

0

NC_006088

1

152732014

A

G

N-Syn

1.00

RNF219

c.794A > G

Q265R

10

-

0

10

0

0

NC_006088

1

153202063

C

T

N-Syn

1.00

SLAIN1

c.1486C > T

G496S

11

0

-

0

11

0

NC_006088

1

166907615

G

C

N-Syn

0.90

NUFIP1

c.925G > C

Q309E

10

0

9

-

0

0

NC_006088

1

169375045

A

G

N-Syn

0.91

SERPINE3

c.254A > G

H85R

11

-

0

10

0

0

NC_006088

1

173852809

T

C

N-Syn

1.00

BRCA2

c.355 T > C

T119A

10

0

10

0

-

0

NC_006088

1

176891377

A

G

N-Syn

1.00

SACS

c.6235A > G

I2079V

11

-

0

11

0

0

NC_006088

1

177772554

C

A

N-Syn

0.86

EFHA1

c.659C > A

A220D

14

12

-

0

0

0

NC_006088

1

177772568

G

A

N-Syn

0.86

EFHA1

c.673G > A

V225I

14

12

0

-

0

0

NC_006088

1

178541726

G

T

N-Syn

0.92

CENPJ

c.2041G > T

V681L

12

0

0

-

11

0

NC_006088

1

187399843

G

A

N-Syn

0.90

GRM5

c.2842G > A

A948T

10

9

0

-

0

0

NC_006088

1

194954389

A

G

N-Syn

1.00

RNF169

c.992A > G

V331A

10

-

0

10

0

0

NC_006089

2

2046630

C

T

N-Syn

1.00

CCDC13

c.860C > T

S287N

12

0

-

0

12

0

NC_006089

2

2059597

T

C

N-Syn

1.00

CCDC13

c.209 T > C

D70G

11

0

11

0

-

0

NC_006089

2

2141930

A

G

N-Syn

0.90

OBSCN

c.17225A > G

I5742T

10

-

0

9

0

0

NC_006089

2

2155796

T

C

N-Syn

1.00

OBSCN

c.14875 T > C

N4959D

11

0

11

0

-

0

NC_006089

2

4669968

C

T

N-Syn

0.90

DLEC1

c.1592C > T

A531V

10

0

-

0

9

0

NC_006089

2

4948035

C

T

N-Syn

1.00

XIRP1

c.4696C > T

A1566T

11

0

-

0

11

0

NC_006089

2

7746258

C

-

Frameshift

1.00

LOC100859401

c.388C > -

Y129fs

10

0

-

0

0

10

NC_006089

2

20725367

C

A

N-Syn

1.00

DBF4

c.1114C > A

P372T

11

11

-

0

0

0

NC_006089

2

21576571

C

T

N-Syn

0.90

C2H7orf63

c.962C > T

T321M

10

0

-

0

9

0

NC_006089

2

23984791

G

A

N-Syn

0.90

PON2

c.521G > A

P174L

10

9

0

-

0

0

NC_006089

2

26789159

T

C

N-Syn

1.00

VWDE

c.2678 T > C

N893S

11

0

11

0

-

0

NC_006089

2

42356129

C

T

N-Syn

1.00

LOC100857506

c.757C > T

P253S

12

0

-

0

12

0

NC_006089

2

43749632

C

T

N-Syn

1.00

TGM4

c.160C > T

A54T

10

0

-

0

10

0

NC_006089

2

47501151

C

A

N-Syn

1.00

SEPT7

c.764C > A

G255V

10

10

-

0

0

0

NC_006089

2

48103938

C

T

N-Syn

1.00

BMPER

c.1957C > T

V653I

11

0

-

0

11

0

NC_006089

2

67476715

T

A

N-Syn

1.00

MYLK4

c.2071 T > A

I691L

12

12

0

0

-

0

NC_006089

2

79168177

C

T

N-Syn

1.00

MTRR

c.2027C > T

R676K

11

0

-

0

11

0

NC_006089

2

96844408

T

G

N-Syn

1.00

CEP192

c.3655 T > G

K1219Q

11

0

0

11

-

0

NC_006089

2

107668292

C

G

N-Syn

1.00

PRKDC

c.3938C > G

C1313S

10

0

-

10

0

0

NC_006089

2

107767247

A

G

N-Syn

0.91

LOC421108

c.77A > G

N26S

11

-

0

10

0

0

NC_006089

2

115050472

C

A

N-Syn

1.00

CSPP1

c.1303C > A

H435N

10

10

-

0

0

0

NC_006089

2

120054459

T

G

N-Syn

1.00

FAM164A

c.605 T > G

V202G

10

0

0

10

-

0

NC_006089

2

126210593

G

A

N-Syn

0.80

C2H8orf38

c.730G > A

V244I

10

8

0

-

0

0

NC_006089

2

148002272

C

T

N-Syn

1.00

TOP1MT

c.1149C > T

M383I

10

0

-

0

10

0

NC_006090

3

18177273

C

T

N-Syn

1.00

EPRS

c.778C > T

H260Y

10

0

-

0

10

0

NC_006090

3

18177438

T

C

N-Syn

1.00

EPRS

c.943 T > C

C315R

11

0

11

0

-

0

NC_006090

3

19964716

A

T

N-Syn

0.90

USH2A

c.9152A > T

E3051V

10

-

0

0

9

0

NC_006090

3

20371026

T

C

N-Syn

0.92

CENPF

c.2726 T > C

E909G

13

0

12

0

-

0

NC_006090

3

20377057

T

T|A

N-Syn

0.75

CENPF

c.[1411 T > T] + [1411 T > A]

N471N, N471Y

12

9

0

0

-

0

NC_006090

3

28850511

A

G

N-Syn

1.00

LOC100858112

c.586A > G

F196L

10

-

0

10

0

0

NC_006090

3

47388200

G

G|A

N-Syn

0.77

ZC3H12D

c.[998G > G] + [998G > A]

T333T, T333M

13

10

0

-

0

0

NC_006090

3

48575253

C

T

N-Syn

0.90

SYNE1

c.11674C > T

A3892T

10

0

-

0

9

0

NC_006090

3

48577869

C

T

N-Syn

0.93

SYNE1

c.11335C > T

D3779N

14

0

-

0

13

0

NC_006090

3

54551285

T

C

N-Syn

1.00

PDE7B

c.868 T > C

T290A

11

0

11

0

-

0

NC_006090

3

66462814

C

T

N-Syn

1.00

LOC421765

c.1076C > T

R359Q

12

0

-

0

12

0

NC_006090

3

66468226

G

T

N-Syn

1.00

LOC421765

c.334G > T

Q112K

10

0

0

-

10

0

NC_006090

3

75929093

G

A

N-Syn

0.93

ZNF292

c.7835G > A

T2612I

14

13

0

-

0

0

NC_006090

3

80234352

G

A

N-Syn

1.00

COL12A1

c.2659G > A

A887T

10

10

0

-

0

0

NC_006091

4

4124961

C

T

Nonsense

1.00

DDX26B

c.151C > T

Q51.

11

0

-

0

11

0

NC_006091

4

9883806

G

A

N-Syn

0.91

SLITRK4

c.1715G > A

R572K

11

10

0

-

0

0

NC_006091

4

49489771

G

T

N-Syn

0.91

RUFY3

c.1588G > T

A530S

11

0

0

-

10

0

NC_006092

5

3898544

C

T

N-Syn

0.80

KIF18A

c.1567C > T

D523N

10

0

-

0

8

0

NC_006092

5

8035275

A

G

N-Syn

1.00

LOC100859209

c.79A > G

C27R

11

-

0

11

0

0

NC_006092

5

20708767

A

G

N-Syn

1.00

API5

c.506A > G

K169R

10

-

0

10

0

0

NC_006092

5

21158570

-

A

Frameshift

0.90

LOC770458

c.105- > A

A35fs

10

9

0

0

0

1

NC_006092

5

22076516

T

C

N-Syn

1.00

C1QTNF4

c.230 T > C

I77T

11

0

11

0

-

0

NC_006092

5

38183079

C

T

N-Syn

0.83

LOC100859479

c.82C > T

P28S

12

0

-

0

10

0

NC_006092

5

44443744

G

G|C

N-Syn

0.75

KIAA1409

c.[2076G > G] + [2076G > C]

Q692H, Q692Q

12

0

9

-

0

0

NC_006092

5

44443754

G

A

N-Syn

0.80

KIAA1409

c.2086G > A

E696K

10

8

0

-

0

0

NC_006092

5

44443755

A

T

N-Syn

0.80

KIAA1409

c.2087A > T

E696V

10

-

0

0

8

0

NC_006092

5

45296293

G

G|A

N-Syn

0.75

C5H14orf49

c.[596G > G] + [596G > A]

A199A, A199V

12

9

0

-

0

0

NC_006092

5

50316949

A

G

N-Syn

1.00

APOPT1

c.440A > G

H147R

12

-

0

12

0

0

NC_006093

6

4563260

G

C

N-Syn

0.90

BMS1

c.1666G > C

L556V

10

0

9

-

0

0

NC_006093

6

15062678

A

G

N-Syn

0.80

PLAU

c.925A > G

W309R

10

-

0

8

0

0

NC_006093

6

25651167

G

A

N-Syn

1.00

RBM20

c.1687G > A

D563N

10

10

0

-

0

0

NC_006093

6

30617911

C

T

N-Syn

0.80

ATE1

c.518C > T

G173D

10

0

-

0

8

0

NC_006093

6

32898174

T

C

N-Syn

1.00

MKI67

c.2414 T > C

M805T

10

0

10

0

-

0

NC_006094

7

9605730

T

C

N-Syn

1.00

ANKRD44

c.584 T > C

K195R

15

0

15

0

-

0

NC_006094

7

18282262

G

G|A

N-Syn

0.75

LRP2

c.[3775G > G] + [3775G > A]

A1259T, A1259A

12

9

0

-

0

0

NC_006094

7

21828274

A

G|A

N-Syn

0.75

CCDC108

c.[2902A > G] + [2902A > A]

N968N, N968D

12

-

0

9

0

0

NC_006094

7

25803714

T

G

N-Syn

0.80

IQCB1

c.952 T > G

T318P

10

0

0

8

-

0

NC_006095

8

1373656

G

A

N-Syn

1.00

CAMSAP1L1

c.1955G > A

A652V

12

12

0

-

0

0

NC_006095

8

2290270

A

G

N-Syn

1.00

LOC100859900

c.65A > G

L22P

13

-

0

13

0

0

NC_006095

8

2506276

C

T

N-Syn

1.00

CRB1

c.1814C > T

S605N

12

0

-

0

12

0

NC_006095

8

2612732

T

C

N-Syn

1.00

ASPM

c.6907 T > C

C2303R

11

0

11

0

-

0

NC_006095

8

7596287

G

T

N-Syn

0.91

NCF2

c.1234G > T

P412T

11

0

0

-

10

0

NC_006095

8

8053190

G

C

N-Syn

0.81

LOC768407

c.875G > C

G292A

16

0

13

-

0

0

NC_006095

8

8188888

T

A

N-Syn

0.82

LOC768392

c.512 T > A

E171V

11

9

0

0

-

0

NC_006095

8

12666139

G

G|A

N-Syn

0.75

ABCA4

c.[4678G > G] + [4678G > A]

V1560I, V1560V

12

9

0

-

0

0

NC_006095

8

23585119

C

G

N-Syn

0.93

LRP8

c.583C > G

G195R

14

0

-

13

0

0

NC_006096

9

800651

G

G|A

N-Syn

0.75

LOC424748

c.[5G > G] + [5G > A]

R2K, R2R

12

9

0

-

0

0

NC_006096

9

2123518

A

G

N-Syn

1.00

YEATS2

c.602A > G

N201S

11

-

0

11

0

0

NC_006096

9

4127341

G

A

N-Syn

1.00

GAL3ST4

c.505G > A

A169T

10

10

0

-

0

0

NC_006096

9

4217231

A

G

N-Syn

0.92

RNF168

c.806A > G

D269G

13

-

0

12

0

0

NC_006096

9

15175477

T

G

N-Syn

1.00

CAPN10

c.1660 T > G

T554P

11

0

0

11

-

0

NC_006096

9

21419266

C

A

N-Syn

0.82

SPTSSB

c.44C > A

P15Q

11

9

-

0

0

0

NC_006097

10

3986458

T

C

N-Syn

0.82

VPS13C

c.3727 T > C

Y1243H

11

0

9

0

-

0

NC_006099

12

9103119

G

A

N-Syn

1.00

COPG

c.1771G > A

A591T

12

12

0

-

0

0

NC_006099

12

15133837

T

C

N-Syn

1.00

LOC100858715

c.89 T > C

V30A

11

0

11

0

-

0

NC_006099

12

19738746

C

T

N-Syn

1.00

NR2C2

c.1061C > T

S354N

10

0

-

0

10

0

NC_006100

13

2703509

A

G|A

N-Syn

0.77

LOC769940

c.[2875A > G] + [2875A > A]

S959P, S959S

13

-

0

10

0

0

NC_006100

13

2703511

A

G|A

N-Syn

0.77

LOC769940

c.[2873A > G] + [2873A > A]

F958S, F958F

13

-

0

10

0

0

NC_006100

13

11337736

C

G

N-Syn

0.90

GEMIN5

c.849C > G

H283Q

10

0

-

9

0

0

NC_006100

13

11349274

A

G

N-Syn

0.83

GEMIN5

c.3739A > G

S1247G

12

-

0

10

0

0

NC_006101

14

5552664

G

A

N-Syn

0.82

TEKT4

c.1192G > A

V398I

11

9

0

-

0

0

NC_006101

14

5975913

T

C

N-Syn

0.93

CHTF18

c.1934 T > C

E645G

14

0

13

0

-

0

NC_006101

14

6002290

G

G|C

N-Syn

0.75

MSLN

c.[774G > G] + [774G > C]

S258S, S258R

12

0

9

-

0

0

NC_006101

14

7697077

C

T

N-Syn

0.80

ABCC6

c.1213C > T

V405M

10

0

-

0

8

0

NC_006101

14

13378210

T

C

N-Syn

0.93

C14H16orf89

c.68 T > C

D23G

14

1

13

0

-

0

NC_006102

15

3706306

T

C

N-Syn

1.00

GLT1D1

c.968 T > C

Q323R

10

0

10

0

-

0

NC_006102

15

4915706

T

C

N-Syn

0.90

ATP6V0A2

c.1246 T > C

I416V

10

0

9

0

-

0

NC_006102

15

4926428

G

A

N-Syn

1.00

LOC100857705

c.1552G > A

R518C

10

10

0

-

0

0

NC_006102

15

5060494

G

A

N-Syn

1.00

MPHOSPH9

c.755G > A

R252K

14

14

0

-

0

0

NC_006102

15

5695994

G

A

N-Syn

0.90

WDR66

c.1690G > A

D564N

10

9

0

-

0

0

NC_006102

15

6317399

C

T

N-Syn

1.00

C15H12orf51

c.7777C > T

D2593N

10

0

-

0

10

0

NC_006102

15

6633596

T

C

N-Syn

1.00

USP30

c.488 T > C

I163T

13

0

13

0

-

0

NC_006102

15

8096384

T

C

N-Syn

1.00

DDX51

c.1493 T > C

M498T

11

0

11

0

-

0

NC_006102

15

8693805

G

C

N-Syn

1.00

RTDR1

c.118G > C

V40L

10

0

10

-

0

0

NC_006104

17

6506143

T

C

N-Syn

0.87

SETX

c.4564 T > C

I1522V

15

0

13

0

-

0

NC_006104

17

6581087

G

A

N-Syn

1.00

C17H9orf171

c.682G > A

D228N

12

12

0

-

0

0

NC_006104

17

6922987

A

G

N-Syn

1.00

ADAMTS13

c.3103A > G

I1035V

12

-

0

12

0

0

NC_006104

17

7858127

A

T

N-Syn

1.00

SEC16A

c.4079A > T

H1360L

15

-

0

0

15

0

NC_006104

17

7905701

G

C

N-Syn

1.00

SNAPC4

c.2609G > C

G870A

11

0

11

-

0

0

NC_006105

18

1082307

C

T

N-Syn

0.90

DNAH9

c.6700C > T

P2234S

10

0

-

0

9

0

NC_006105

18

1111244

G

A

N-Syn

0.80

DNAH9

c.8491G > A

V2831M

10

8

0

-

0

0

NC_006105

18

6605385

C

G

N-Syn

1.00

ATAD5

c.3652C > G

P1218A

11

0

-

11

0

0

NC_006105

18

6605422

G

A

N-Syn

1.00

ATAD5

c.3689G > A

R1230K

10

10

0

-

0

0

NC_006105

18

6967029

C

T

N-Syn

1.00

C18H17orf58

c.1018C > T

L340F

12

0

-

0

12

0

NC_006106

19

5858876

T

C

N-Syn

1.00

ERAL1

c.1186 T > C

M396V

14

0

14

0

-

0

NC_006106

19

6213750

G

C

N-Syn

1.00

SLC6A4

c.242G > C

A81G

10

0

10

-

0

0

NC_006106

19

7495965

C

G

N-Syn

0.82

BRIP1

c.1718C > G

P573R

11

0

-

9

0

0

NC_006107

20

12338968

T

G

N-Syn

0.83

CASS4

c.1169 T > G

N390T

12

0

0

10

-

0

NC_006107

20

12696859

T

A

N-Syn

1.00

CYP24A1

c.878 T > A

L293Q

12

12

0

0

-

0

NC_006108

21

2336588

G

A

Nonsense

0.80

TAS1R3

c.1108G > A

R370.

10

8

0

-

0

0

NC_006108

21

3215527

C

T

N-Syn

0.92

ENO1

c.1265C > T

R422H

12

0

-

0

11

0

NC_006108

21

4657639

G

A

N-Syn

1.00

KIAA0090

c.2716G > A

R906C

11

11

0

-

0

0

NC_006110

23

5163924

T

C

N-Syn

1.00

ZBTB8A

c.232 T > C

F78L

10

0

10

0

-

0

NC_006112

25

1498400

G

A

N-Syn

1.00

HORMAD1

c.844G > A

A282T

11

11

0

-

0

0

NC_006113

26

4679877

G

A

N-Syn

1.00

LOC768535

c.1097G > A

P366L

10

10

0

-

0

0

NC_006127

Z

71529316

G

A

N-Syn

1.00

DMXL1

c.4394G > A

A1465V

11

11

0

-

0

0

  1. Contig ID, chromosome (Chr) numbers, reference position (Ref Pos), reference base (Ref Base), called (SNP) base, impact (kinds of protein mutation), SNP%, feature name (gene name), DNA change, amino acid (AA) change, Depths, and five columns for SNP counts (cnts) are indicated.