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Table 1 Summary of inter-and intra-genic SNPs in 35 chickpea genotypes

From: Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.)

Genotype

Intergenic

No of intragenic SNPs

Others

 

No. of intergenic

Intron

Exon

 

No. of intronic SNPs

Non-synonymous

Synonymous

 

No. of non-synonymous coding

No. of non-synonymous start

No. of start lost

No. of stop gained

No. of stop lost

No. of synonymous coding

No. of synonymous stop

Total

Arerti

95,463

11,373

1,836

1

2

23

10

1,906

2

967

111,583

C 104

141,435

18,636

2,887

2

2

31

8

3,180

1

1,194

167,376

C 214

111,023

13,121

2,094

2

5

30

11

2,221

2

902

129,411

Ejerie

84,715

10,047

1,719

0

4

18

10

1,786

2

964

99,265

ICC 1431

126,604

16,306

2,456

1

5

25

12

2,828

3

1,007

149,247

ICC 1496

99,289

11,615

1,807

2

3

19

6

1,992

2

843

115,578

ICC 1882

107,060

12,517

1,936

3

3

23

11

2,101

5

882

124,541

ICC 283

109,146

13,296

1,943

1

3

24

10

2,130

2

861

127,416

ICC 3137

172,561

20,255

3,189

1

8

45

20

3,428

6

1,314

200,827

ICC 4958

292,686

35,022

5,159

3

13

58

19

5,884

8

1,951

340,803

ICC 506

169,681

19,028

2,977

4

7

32

15

3,292

6

1,358

196,400

ICC 6263

151,707

14,874

2,394

1

7

38

15

2,481

5

1,405

172,927

ICC 8261

151,627

16,987

2,586

1

7

30

10

2,802

4

1,290

175,344

ICC 995

146,193

15,647

2,428

1

8

25

14

2,748

3

1,247

168,314

ICCV 00108

110,493

11,327

1,442

2

3

19

6

1,459

2

927

125,680

ICCV 03312

118,283

12,341

1,996

0

5

30

10

2,142

3

1,123

135,933

ICCV 04112

133,378

17,305

2,383

1

7

30

8

2,712

4

1,093

156,921

ICCV 04516

84,366

8,806

1,385

2

3

20

7

1,565

0

937

97,091

ICCV 05530

107,685

12,448

1,942

1

7

31

13

2,055

3

995

125,180

ICCV 10

151,630

17,308

2,251

1

3

24

6

2,416

6

999

174,644

ICCV 97105

222,311

28,993

4,029

3

7

35

12

4,766

7

1,243

261,406

IG 72933

528,292

87,348

11,343

5

27

80

35

15,069

19

2,236

644,454

IG 72953

779,323

166,944

21,356

5

29

119

53

31,241

48

2,626

1,001,744

ILC 3279R

98,538

9,967

1,845

1

1

30

12

1,820

2

1,092

113,308

JAKI 9218

271,934

31,648

4,530

2

11

49

14

5,105

5

1,734

315,032

JG 11

180,028

21,190

2,559

2

5

27

7

2,761

4

1,202

207,785

JG 130

143,400

16,890

2,501

2

6

27

4

2,781

5

1,046

166,662

JG 16

126,104

15,899

2,238

2

5

27

11

2,437

5

887

147,615

JG 62

172,088

20,888

3,224

1

9

38

16

3,580

6

1,017

200,867

JG 74

146,466

18,427

2,743

1

5

27

12

3,147

6

1,154

171,988

KAK 2

125,250

13,638

2,041

1

5

30

9

2,253

3

1,130

144,360

PI 489777

530,227

99,288

12,742

5

24

94

32

17,737

24

2,032

662,205

Pb 7

169,234

18,338

2,800

2

6

37

11

3,010

7

1,245

194,690

Vijay

138,673

16,769

2,715

2

6

33

17

2,929

3

1,343

162,490

WR 315

158,812

20,911

3,102

2

4

32

17

3,550

6

934

187,370