Table 2.
Evaluation metrics of transcriptomes
| Parameters | Assembly v1.0a | Genome guided | Assembly v2.0 |
|---|---|---|---|
| Sequence numbers | 84,882 | 80,473 | 49,058 |
| General metrics (bp) | |||
| Mean contig length | 1214.4 | 777.5 | 1438.9 |
| N50 | 1591 | 1353 | 1795 |
| N90 | 605 | 289 | 804 |
| Sequence length ranges (%) | |||
| ≤500 bp | 19.0 | 55.8 | 11.5 |
| 501–1000 bp | 32.1 | 18.0 | 26.3 |
| 1001–1500 bp | 20.7 | 11.1 | 23.9 |
| 1501–2000 bp | 13.2 | 7.3 | 17.4 |
| 2001–2500 bp | 7.2 | 3.7 | 9.8 |
| 2501–3000 bp | 3.6 | 1.9 | 4.9 |
| >3000 bp | 4.2 | 2.2 | 6.2 |
| Transcriptome size (Mb) | 103.1 | 62.6 | 70.6 |
| Read mapping back (%) | |||
| Mapped | 95.9 | 90.7 | 93.4 |
| Proper pairb | 81.2 | 77.2 | 82.9 |
| BUSCO evaluation (%)c | |||
| Completeness | 89.8 | 82.0 | 92.4 |
| Single copy | 65.6 | 62.8 | 80.6 |
| Duplicated | 24.2 | 19.2 | 10.8 |
| Fragmented | 3.9 | 4.7 | 2.5 |
| Missing | 6.3 | 13.3 | 4.9 |
| Transcript completeness (%)d | |||
| Full length | 16.7 | 18.7 | 37.7 |
| Nearly full length | 41.7 | 42.9 | 72.9 |
aPreviously published C. endivia transcriptome assembly19
bRead pairs mapping to the same transcript
cTotal BUSCO groups searched were 1440 from the Embryophyta_odb9 database
dPercentage of (nearly- and full-length) transcripts with 70–100% alignment coverage versus respective hits in the NCBI Refseq protein dataset