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Table 2 The basic information of 21 Primulina RAD-Seq data related to chloroplast genomes

From: The complete chloroplast genome of Primulina and two novel strategies for development of high polymorphic loci for population genetic and phylogenetic studies

Species

ID

Reads No.a

Quality Q30b

RAD tags No.c

Paired tags No. - ratio (%)d

Overlap tags No. - ratio (%)e

Paired & Overlap tags No. - ratio (%)f

Cpcontigsg

No.

Length

Ratio (%)h

P. eburnea

CZYX01–1

320,451

96.0; 97.2

164

73 (×2) - 89

132 - 80

50 (×2) - 61

62

69,862

55.1

CZYX01–2

239,167

96.3; 95.7

151

64 (×2) - 85

130 - 86

52 (×2) - 69

62

65,591

51.7

CZYX01–3

426,610

94.7; 96.1

151

61 (×2) - 81

121 - 80

44 (×2) - 58

75

63,584

50.1

CZYX01–4

474,623

95.4; 96.4

153

63 (×2) - 82

119 - 78

43 (×2) - 56

76

62,588

49.3

CZYX01–5

797,450

95.4; 96.6

148

59 (×2) - 80

115 - 78

40 (×2) - 54

79

65,103

51.3

CZYX01–6

427,701

96.4; 95.6

154

64 (×2) - 83

126 - 82

48 (×2) - 62

70

67,315

53.0

CZYX01–7

404,182

96.4; 96.3

156

67 (×2) - 86

129 - 83

50 (×2) - 64

65

66,895

52.7

CZYX01i

441,455

95.8; 96.3

154

64 (×2) - 84

125 - 81

47 (×2) - 61

70

65,848

51.9

P. danxiaensis

CZYX02–1

278,229

96.2; 97.4

145

58 (×2) - 80

117 - 81

42 (×2) - 58

68

62,883

49.6

CZYX02–2

343,741

96.0; 96.1

145

61 (×2) - 84

111 - 77

44 (×2) - 61

69

65,103

51.3

CZYX02–3

228,868

96.2; 95.5

137

52 (×2) - 76

109 - 80

38 (×2) - 55

72

58,660

46.2

CZYX02–4

230,025

96.2; 95.4

138

53 (×2) - 77

110 - 80

38 (×2) - 55

72

58,696

46.3

CZYX02–5

211,979

96.3; 95.6

140

56 (×2) - 80

115 - 82

46 (×2) - 66

71

61,728

48.6

CZYX02–6

227,541

96.3; 96.5

145

59 (×2) - 81

117 - 81

44 (×2) - 61

69

61,609

48.6

CZYX02–7

277,044

96.3; 96.5

143

57 (×2) - 80

111 - 78

42 (×2) - 59

75

63,284

49.9

CZYX02j

256,775

96.2; 96.1

142

57 (×2) - 80

113 - 80

43 (×2) - 59

71

61,709

48.6

P. juliae

CZYX03–1

208,356

95.9; 96.0

141

60 (×2) - 85

114 - 81

42 (×2) - 60

61

63,457

50.0

CZYX03–2

315,085

95.9; 95.9

142

60 (×2) - 85

109 - 77

40 (×2) - 56

65

64,130

50.5

CZYX03–3

172,588

96.1; 96.7

139

54 (×2) - 78

110 - 79

39 (×2) - 56

71

65,415

51.6

CZYX03–4

145,876

96.3; 96.1

139

54 (×2) - 78

116 - 83

45 (×2) - 65

68

61,485

48.5

CZYX03–5

694,697

96.3; 97.4

155

65 (×2) - 84

126 - 81

40 (×2) - 52

69

65,392

51.5

CZYX03–6

333,471

96.1; 97.1

154

63 (×2) - 82

129 - 84

52 (×2) - 68

67

69,166

54.5

CZYX03–7

381,048

95.9; 96.0

140

58 (×2) - 83

112 - 80

41 (×2) - 59

61

63,551

50.1

CZYX03k

321,589

96.1; 96.5

144

59 (×2) - 82

117 - 81

43 (×2) - 59

65

64,647

51.0

  1. aReads No. was counted from the Reads which was mapped into the reference cp genome P.eburnea (WHY01), instead of whole sequencing data.
  2. bQuality Q30 was counted from Read1 and Read2 respectively.
  3. cRAD tags No.: The number of Tag1s, clustered from read1 of RAD-Seq.
  4. dPaired tags No. & ratio: The number of pTs (paired tags) and the value of pTs No. / RAD tags No., where pT was mixed from two Tag1s at forward and reverse directions of the same RE (restriction enzyme site).
  5. eOverlap tag No. & ratio: The number of oTs (overlap tags) and the value of oTs No. / RAD tags No., where oT was mixed from Tag1 and its paired Tag2 (assembly of read2) according to the overlap.
  6. fPaired & Overlap tags No. & ratio: The number of poTs (paired & overlap tags) and the value of poTs No. / RAD tags No., where poT was mixed from paired tags (two Tag1s) and their paired Tag2s (two Tag2s). Both of two Tag1 have overlap regions with paired Tag2s.
  7. gCpcontigs: it is a longer sequences without unknown nucleotides, and it was assembled from all the kinds of tags, including pTs, oTs, poTs and other types, according to the their position and overlap information.
  8. hRatio: it was counted as following: The length of Cpcontigs / the length of reference cp genome of P.eburnea (WHY01), while the cp genome length here is 126,890, excluding the length of IRa.
  9. iCZYX01, jCZYX02, kCZYX03: they represent the index in the species level, which was calculated by the average level of 7 individuals from the same species