Table 3 De novo transcriptome assemblies and classification of the assembled cork oak transcripts

Contigs

104,862

33,034

80,357

Contigs > 500 bp

54,764 (52.2 %)

26,313 (79.6 %)

50,197 (62.5 %)

Contigs < 200 bp

6,306 (6 %)

481 (1.5 %)

4,510^a

Contigs with homologous in Uniprot

73,103 (69.7 %)

26,951 (81.6 %)

56,517 (70.3 %)

Unique Uniprot IDs

28,154 (38.5 %)

16,047 (48.6 %)

24,474 (43.3 %)

Complete contigs

16,149 (15.4 %)

12,953 (39.2 %)

19,146 (23.8 %)

C-terminus contigs

15,818 (15.1 %)

5,342 (16.2 %)

11,410 (14.2 %)

N-terminus contigs

15,368 (14.7 %)

4,064 (12.3 %)

10,108 (12.6 %)

Internal contigs

25,432 (24.2 %)

4,575 (13.8 %)

15,509 (19.3 %)

Misassembled contigs

336 (0.32 %)

17 (0.05 %)

344 (0.43 %)

Contigs without UNIPROT homologous

31,759 (30.3 %)

6,083 (18.40 %)

23,840 (29.6 %)

Novel genes

5,388 (5.14 %)

1,320 (4 %)

4,658 (5.8 %)

Complete ORF

2,758 (2.6 %)

664 (2.01 %)

2,318 (2.9 %)

Partial ORF

2,630 (2.5 %)

656 (1.99 %)

2,340 (2.9 %)

Unknown contigs

26,346 (25.1 %)

4,757 (14.4 %)

19,163 (23.8 %)

Unknown contigs < 200 bp

5,471 (5.2 %)

407 (1.2 %)

0^a

Putative ncRNAs

25 (0.02 %)

6 (0.02 %)

19 (0.02 %)

Reads mapped^b

2,020,921 (96.8 %)

1,909,842 (91.5 %)

2,009,759 (96.2 %)

Unique mapped reads

1,703,996 (84.3 %)

1,549,803 (74,2 %)

1,491,131 (71.4 %)

Duplicated mapped reads

273,619 (13.1 %)

270,027 (14.1 %)

367,486 (17.6 %)

Mapping more than two times

43,306 (2.1 %)

90,012 (4.7 %)

151,142 (7.2 %)

Average coverage

7.8

14.2

8