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. 2019 Jun 5;9(8):2723–2737. doi: 10.1534/g3.119.400229

Table 1. Quality filtering and statistics of raw reads obtained in transcriptome libraries of B. napus exposed to low-temperature treatments.

Sample name Raw reads Clean reads clean bases Error rate (%) Q20 (%) Q30 (%) GC content (%)
HX17_MA1 61608094 58966572 8.84G 0.03 97.36 92.93 44.06
HX17_MA2 46842038 45252272 6.79G 0.03 96.98 92.17 44.39
HX17_MA3 51620482 50405900 7.56G 0.03 97.11 92.01 45.91
HX17_CA1 45028428 44096512 6.61G 0.03 96.97 91.66 45.83
HX17_CA2 53540226 52633174 7.89G 0.03 96.72 91.49 46.35
HX17_CA3 49776538 47962390 7.19G 0.03 96.70 91.54 43.39
HX17_FA1 46114476 45390992 6.81G 0.03 96.66 91.37 44.84
HX17_FA2 66471914 64442766 9.67G 0.03 97.11 92.40 45.85
HX17_FA3 49756338 49191330 7.38G 0.03 97.20 92.53 45.64
HX17_MB1 45873106 45028940 6.75G 0.03 95.42 88.17 44.09
HX17_MB2 47889494 47067140 7.06G 0.03 96.75 91.57 45.00
HX17_MB3 46228026 45344394 6.80G 0.03 96.94 92.04 44.25
HX17_CB1 70149774 68467860 10.27G 0.03 97.85 94.12 44.40
HX17_CB2 54975576 53977612 8.10G 0.03 97.12 92.04 44.50
HX17_CB3 55136028 53840712 8.08G 0.03 97.02 91.82 44.74
HX17_FB1 79518680 78163306 11.72G 0.03 97.70 93.70 44.76
HX17_FB2 48126142 47147508 7.07G 0.03 96.75 91.28 44.80
HX17_FB3 52485614 51527762 7.73G 0.03 97.77 93.79 44.19
HX58_MA1 67391320 65727088 9.86G 0.03 97.16 92.16 44.28
HX58_MA2 66677164 64776152 9.72G 0.03 97.09 91.98 43.86
HX58_MA3 47017928 44892330 6.73G 0.03 97.07 92.07 43.88
HX58_CA1 44491830 43128444 6.47G 0.03 96.66 91.39 46.46
HX58_CA2 47877742 46243718 6.94G 0.03 96.73 91.40 45.62
HX58_CA3 49056666 47594184 7.14G 0.03 97.85 93.99 45.77
HX58_FA1 77825480 76080646 11.41G 0.03 97.92 94.08 44.84
HX58_FA2 72714882 70675296 10.6G 0.03 97.72 93.61 45.33
HX58_FA3 62524530 60787534 9.12G 0.03 97.71 93.59 45.10
HX58_MB1 55247676 54098192 8.11G 0.03 96.74 91.23 44.28
HX58_MB2 57837196 56764648 8.51G 0.03 96.82 91.34 45.16
HX58_MB3 49353542 48225898 7.23G 0.03 97.34 92.54 44.69
HX58_CB1 61754716 60061840 9.01G 0.03 97.88 93.95 43.42
HX58_CB2 66709668 64672348 9.70G 0.03 97.69 93.60 42.76
HX58_CB3 52648416 51400508 7.71G 0.03 96.73 91.28 43.77
HX58_FB1 58213716 56978060 8.55G 0.03 97.04 91.89 46.07
HX58_FB2 59190884 57729982 8.66G 0.03 97.11 92.37 46.39
HX58_FB3 60769766 59189468 8.88G 0.03 97.10 92.36 45.06
Assembly Steps Total assembled transcripts Number of transcripts (>1000bp) Percent of transcripts Maximum transcript length Average transcript length N50 value (bp) Coverage (X)
Assembler SOAPdenovotrans (65 k-mer) 91,765 32,509 35.43 12,805 903.39 1,427 160
After gap filling and hierarchical clustering 53,806 24,429 45.40 12,674 1,096.96 1,499 218
After removing mis-assembled transcripts 46,556 19,347 41.55 9,811 1,013.66 1,393 226
BLASTX best group representatives (unigenes) 25,400 12,588 49.56 9,811 1,153.30 1,502 240