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