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Table 2 Sequencing metrics for Cedrela and Meliaceae samples

From: Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives

Specimen

SRA Accession

Sequence Yield

On-Target Yield

On-Target (%)

Chloroplast (CP) Yield

CP (%)

CP Depth

CP (%) Covered

‘N’ Bases (%)

C. angustifolia 88

SRS3532111

1,515,526

488,207

32.2

248,243

16.4

157

100.0

0.1

C. angustifolia 143

SRS3532109

8,462,020

3,191,296

37.7

901,138

10.6

568

100.0

0.1

C. fissilis 9

SRS3532073

1,174,195

286,398

24.4

93,257

7.9

59

99.9

0.2

C. fissilis 19

SRS3531955

5,431,374

2,122,651

39.1

333,680

6.1

210

99.9

0.2

C. fissilis 112

SRS3532019

1,750,937

376,881

21.5

151,391

8.6

96

99.8

0.4

C. fissilis 130

SRS3532093

5,351,355

2,154,295

40.3

135,883

2.5

86

99.9

0.2

C. fissilis 140

SRS3532018

12,183,129

5,047,225

41.4

403,902

3.3

255

100.0

0.1

C. fissilis 211

SRS3532001

1,272,124

259,059

20.4

167,826

13.2

106

100.0

0.2

C. fissilis 230

SRS3532122

3,251,712

1,183,526

36.4

106,353

3.3

67

99.9

0.4

C. fissilis 254

SRS3532102

17,394,724

5,583,057

32.1

643,227

3.7

405

100.0

0.1

C. fissilis 264

SRS3532060

19,290,108

7,776,152

40.3

356,979

1.9

225

100.0

0.1

C. fissilis 292

SRS3532121

7,116,518

2,752,495

38.7

1,866,075

26.2

1176

100.0

0.1

C. montana 50

SRS3532121

5,561,468

2,026,840

36.4

577,438

10.4

364

100.0

0.2

C. odorata 10

SRS3532068

4,009,101

1,472,131

36.7

273,812

6.8

173

99.8

0.4

C. odorata 52

SRS3532030

12,254,507

4,791,273

39.1

618,594

5.0

390

100.0

0.1

C. odorata 162

SRS3531967

8,942,300

3,574,795

40.0

756,725

8.5

477

100.0

0.1

C. odorata 185

SRS3532120

5,713,214

2,177,026

38.1

382,876

6.7

241

100.0

0.1

C. odorata 202

SRS3532089

6,372,915

2,366,009

37.1

116,791

1.8

74

99.7

0.4

C. odorata 222

SRS3532005

10,421,206

4,017,316

38.5

289,695

2.8

183

99.8

0.3

C. odorata 277

SRS3531957

6,794,076

2,539,070

37.4

309,154

4.6

195

99.8

0.5

C. odorata 287

SRS3532135

438,310

6566

1.5

35,604

8.1

25

90.2

7.7

C. saltensis 75

SRS3532020

29,081,506

10,692,874

36.8

831,948

2.9

524

100.0

0.1

C. saltensis 102

SRS3532010

5,252,123

2,107,682

40.1

672,165

12.8

424

100.0

0.1

C. saltensis 186

SRS3532110

1,829,249

554,830

30.3

125,974

6.9

79

100.0

0.2

G. guidonia 2

SRS3532153

5,211,243

68,501

1.3

92,122

1.8

78

74.2

19.5

G. guidonia 4

SRS3532152

6,710,368

100,652

1.5

129,500

1.9

105

77.8

13.9

G. guidonia 7

SRS3532151

6,850,155

101,252

1.5

81,731

1.2

74

69.8

17.8

G. guidonia 9

SRS3532150

14,213,046

206,827

1.5

197,446

1.4

139

89.3

13.5

G. guidonia 10

SRS3532124

7,833,412

91,070

1.2

69,582

0.9

69

63.9

15.0

G. guidonia 11

SRS3532123

9,166,583

123,598

1.3

279,357

3.0

194

90.9

7.3

G. guidonia 13

SRS3532149

9,909,255

133,845

1.4

259,749

2.6

184

88.9

7.6

G. guidonia 15

SRS3532148

10,634,632

148,498

1.4

267,334

2.5

185

91.1

7.6

G. guidonia 17

SRS3532147

10,900,380

128,635

1.2

138,537

1.3

108

80.8

13.3

G. guidonia 19

SRS3532146

16,194,976

195,256

1.2

342,985

2.1

229

94.5

8.3

S. mahagoni 21

SRS3532156

16,927,562

1,051,671

6.2

1,530,129

9.0

966

99.8

1.5

S. mahagoni 22

SRS3532155

18,098,858

1,113,548

6.2

3,806,990

21.0

2399

100.0

0.5

T. tuberculata 1

SRS3531991

3,823,599

39,222

1.0

54,256

1.4

159

89.8

17.1

T. tuberculata 3

SRS3531995

5,915,718

60,793

1.0

92,170

1.6

76

76.4

14.2

T. tuberculata 6

SRS3531996

6,159,511

63,116

1.0

140,155

2.3

110

80.0

11.4

T. tuberculata 8

SRS3531994

6,595,654

70,395

1.1

59,560

0.9

50

74.4

23.5

T. tuberculata 12

SRS3531993

11,354,222

92,063

0.8

283,424

2.5

56

60.9

8.3

T. tuberculata 18

SRS3531989

10,145,721

103,682

1.0

225,870

2.2

196

91.3

12.2

T. tuberculata 20

SRS3531990

8,374,551

91,146

1.1

117,705

1.4

90

82.5

13.2

  1. Metrics include: SRA Accession number; total sequence yield (in bp), sequenced reads with identity to the gene target (‘On-Target Yield’, in bp); percent of sequenced reads with gene target identity (‘On-Target (%)’); sequenced reads with chloroplast identity (‘Chloroplast (CP) Yield’, in bp); percent of sequenced reads with CP identity (‘CP (%)’); depth of coverage across the CP reference genome (‘CP Depth’); the percentage of the CP reference genome covered at 1X depth (‘CP [%] Covered’); and the percentage of ‘N’ bases in the specimen chloroplast genome (‘N’ Bases [%])
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BMC Genomics

ISSN: 1471-2164

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