RNA-Seq analysis and transcriptome assembly for blackberry (Rubus sp. Var. Lochness) fruit

BMC Genomics

Table 1 Summary of de novo assembly of transcriptome sequence reads without reference genome

Samples	Total raw reads	Total clean reads	Total clean nucleotides (nt)	Q20 percentage	GC percentage	Type of gene detected	Total number	Total length (nt)	Mean length (nt)	N50
RF1	48 335 970	44 166 280	4 416 628 000	96,59%	45,65%	Raw sequences	68 768	32 762 368	476	1284
RF1	48 335 970	44 166 280	4 416 628 000	96,59%	45,65%	Consensus sequences	41 770	37 272 781	892	1627
RF2	49 872 928	45 562 458	4 556 245 800	96,55%	45,91%	Raw sequences	68 357	33 018 028	483	1289
RF2	49 872 928	45 562 458	4 556 245 800	96,55%	45,91%	Consensus sequences	41 881	37 472 313	895	1611

First column shows the total raw reads, the next columns shows the clean reads and nucleotids. Q20 percentage column shows the proportion of nucleotides with quality value larger than 20. GC percentage is proportion of guanidine and cytosine nucleotides among total nucleotides. The total number column shows the total sequences obtained, that represents the all raw sequences and consensus sequences, respectively. Next columns show the total nucleotides length and their mean length. The last column shows the N50 value (defined as the length for which the collection of all sequences of that length or longer contains at least half of the sum of the lengths of all sequences).

ISSN: 1471-2164