Table 1 RNA-sequencing and de novo assembly statistics
Trimming statistics | Â | Â |
|---|---|---|
Number of reads before trimming | Â | 57,059,700 |
Number of reads after trimming | Â | 52,770,704 |
Sequences discarded during trimming | Â | 7.52% |
Average length before trimming | Â | 94.5Â bp |
Average lenth after trimming | Â | 97.3Â bp |
Number of reads per sample | Â | Â |
T1 non-toxic strain-fed (AL1T) | Â | 6,102,912 |
T1 toxic strain-fed (AL9T) | Â | 14,571,224 |
T2 non-toxic strain-fed (AL1T) | Â | 16,419,080 |
T2 toxic strain-fed (AL9T) | Â | 15,678,278 |
Additional sequences used for the assembly | Â | Â |
Illumina (digestive gland) | Â | 49,871,662 |
454 (various tissues) | Â | 115,557 |
Sanger (various tissues, Mytibase collection) | Â | 18,788 |
Trinity assembly statistics | all contigs | longest transcript per gene |
Assembly size | 16,350,006Â bp | 11,571,682Â bp |
Total number of contigs | 21,193 | 12,079 |
Mapping rate | 59.04% | 52.00% |
Non-specific matches | 4.29% | 0.00% |
N50 | 1,010 | 1,216 |
Mean contig length | 771Â bp | 958Â bp |
Longest contig | 14,931Â bp | 14,931Â bp |
Annotation statistics (longest transcript per gene model) | Â | Â |
Contigs with BLAST hit vs UniProtKB/Swiss-Prot | Â | 5,818 (48.1%) |
Contigs with BLAST hit vs C. gigas predicted proteins | Â | 7,227 (59.8%) |
Contigs with BLAST hit vs P. fucata predicted proteins | Â | 6,943 (57.5%) |
Contigs with BLAST hit vs L. gigantea predicted proteins | Â | 6,699 (55.5%) |
Contigs with InterPro domains | Â | 5,432 (45.0%) |
Contigs with PFAM domains | Â | 5,696 (47.2%) |
Contigs with eggNOG terms | Â | 4,524 (37.5%) |
Contigs with GO Cellular Component terms | Â | 4,920 (40,7%) |
Contigs with GO Biological Process terms | Â | 4,207 (34.8%) |
Contigs with GO Molecular Fuction terms | Â | 4,236 (35.1%) |