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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