Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors

BMC Genomics

Table 1 Detailed Information on the Assembly Results.

Newbler Reads
Total number of reads	3,160,306
Number of aligned reads	2,708,437
Number of aligned bases	990,882,504
Number of wholly assembled reads	2,326,354
Number of partially assembled reads	374,202
Number of singletons	235,486
Number of repetitive reads	12,291
Number of outlier reads	139,210
Number of too-short reads	72,763
Newbler Contigs
Total number of contigs	110,031
Total number of contig bases	55,246,326
Average coverage	17.9×
Average contig size	502 bp
Contig N50	829 bp
Number of contigs with size > 100 bp	90,417
Number of contigs with size > 500 bp	42,767
Largest contig Size	16,649 bp
Newbler Isotigs
Total number of isotigs	83,166
Average contig count	3.7
Largest contig count	29
Number of isotigs with one contig	28,111
Average isotig size	1,337 bp
Isotig N50	1,639 bp
Largest isotig Size	24,959 bp
Newbler Isogroups
Total number of isogroups	41,879
Average isotig count	2.0
Average contig count	2.6
Largest isotig count	649
Largest contig count	2,491
Number of isogroups with one isotig	28,615
Number of isogroups with one contig	27,530
MIRA3 assembly of Newbler singletons
Reads assembled	91,926
Number of contigs	37,143
Contig N50	486
Largest contig size	1604

ISSN: 1471-2164