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Table 1 RADseq results in 18 plants using Hi-seq 2000 NGS platform

From: Identification of sex-linked SNP markers using RAD sequencing suggests ZW/ZZ sex determination in Pistacia vera L.

Parents and F1 plants

Read number

Total RAD sequence (bp)*

Number of RAD tags

Total sequence of RAD taqs (bp)**

Coverage depth***

Sequence coverage****

GC rate (%)

Total SNP

Heterozygous SNP rate (%)

Females

         

Siirt

15,873,498

1,301,626,836

422,422

34,638,604

37.6

2.0

37.65

90,999

17.3

P-F-1

24,754,856

2,029,898,192

442,751

36,305,582

55.9

3.1

37.12

98,348

26.9

P-F-2

22,527,994

1,847,295,508

513,815

42,132,830

43.8

2.8

37.60

97,562

28.0

P-F-3

28,035,806

2,298,936,092

513,654

42,119,628

54.6

3.5

37.07

99,776

25.3

P-F-4

33,578,112

2,753,405,184

560,479

45,959,278

59.9

4.2

36.86

101,339

30.5

P-F-5

23,563,272

1,932,188,304

539,390

44,229,980

43.7

2.9

37.47

98,767

31.9

P-F-6

23,374,790

1,916,732,780

523,591

42,934,462

44.6

2.9

37.38

98,876

29.9

P-F-7

28,326,906

2,322,806,292

539,702

44,255,564

52.5

3.5

36.88

100,355

27.4

P-F-8

25,474,290

2,088,891,780

431,895

35,415,390

59.0

3.2

37.64

96,551

17.5

Subtotal

225,509,524

18,491,780,968

4,487,699

367,991,318

451.6

28.0

-

882,573

-

Subaverage

25,056,614

2,054,642,330

498,633

40,887,924

50.2

3.1

37.30

98,064

26.1

Males

         

Bağyolu

27,187,532

2,229,377,624

552,533

45,307,706

49.2

3.4

38.00

79,746

33.1

P-M-1

22,615,328

1,854,456,896

498,044

40,839,608

45.4

2.8

36.98

98,046

27.2

P-M-2

10,108,252

828,876,664

422,176

34,618,432

23.9

1.3

37.10

75,521

20.5

P-M-3

19,417,040

1,592,197,280

541,272

44,384,304

35.9

2.4

37.48

95,941

26.7

P-M-4

11,079,312

908,503,584

410,036

33,622,952

27.0

1.4

38.77

72,909

18.6

P-M-5

38,882,284

3,188,347,288

657,285

53,897,370

59.2

4.8

37.65

102,340

30.5

P-M-6

26,158,302

2,144,980,764

569,710

46,716,220

45.9

3.2

37.58

100,049

27.0

P-M-7

29,947,304

2,455,678,928

596,268

48,893,976

50.2

3.7

37.51

99,531

27.5

P-M-8

39,817,004

3,264,994,328

623,841

51,154,962

63.8

4.9

37.41

103,115

27.8

Subtotal

225,212,358

18,467,413,356

4,871,165

399,435,530

400.6

28.0

-

827,198

-

Subaverage

25,023,595

2,051,934,817

541,241

44,381,726

44.5

3.1

37.61

91,911

26.5

Total

450,721,882

36,959,194,324

9,358,864

767,426,848

852.2

56.0

 

1,709,771

 

Average

25,040,105

2,053,288,574

519,937

42,634,825

47.3

3.1

37.45

94,987

26.3

  1. *Total RAD sequence was calculated by multiplying read number by 82 bp read length of Illumina.
  2. **Total sequence of RAD taqs was calculated by multiplying number of RAD tags by Illumina 82 bp read length.
  3. ***Coverage depth was calculated by dividing Illumina read number by number of RAD taqs.
  4. ****Sequence coverage was calculated by dividing total RAD sequence (bp) by the estimated genome size (660 Mbp) of pistachio.
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BMC Genomics

ISSN: 1471-2164

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