Table A5.
Values pertaining to the RNA-Seq output, its trimming and assembly and the transcript length distributions.
| Read Trimming and Clipping of Adapters | |
| Raw Paired Reads a | 70,409,091 |
| Surviving Paired Reads b | 64,038,268 |
| Surviving Paired Reads c (%) | 91 |
| Normalization | |
| Surviving Paired Reads after normalization d | 8,945,044 |
| Surviving Paired Reads after normalization e (%) | 14 |
| Trinity de novo Assembly | |
| Number of Transcripts | 148,563 |
| Number of Components f | 86,994 |
| Total Transcripts Length (bp) | 126,994,523 |
| Max. Transcript Length (bp) | 15,491 |
| Min. Transcript Length (bp) | 224 |
| Median Transcript Length (bp) | 514 |
| Mean Transcript Length (bp) | 854 |
| N50 (bp) | 1360 |
| BLAST Annotation and Filtered Annotated Components | |
| Number of Transcripts g | 8866 |
| Number of Components | 3802 |
| Total Transcripts Length (bp) | 15,030,163 |
| Max. Transcript Length (bp) | 8887 |
| Min. Transcript Length (bp) | 297 |
| Median Transcript Length (bp) | 1504 |
| Mean Transcript Length (bp) | 1695 |
| N50 (bp) | 2043 |
a Number of paired reads obtained from the sequencer; b number of remaining paired reads after the trimming step; c percentage of surviving paired reads/raw paired reads; d number of remaining paired reads after the normalization step; e percentage of surviving paired reads after normalization/surviving paired reads after trimming; f a component is a family of similar transcripts, most likely RNA variants of the same family; g each transcript has been aligned against the uniprot_sprot.trinotate_v2.0.pep protein database using the blastx program from the NCBI BLAST family.