Table 1.
Summary of genome and liver transcriptome statistics of the European sardine, Sardina pilchardus.
| Features | Genome # | Liver Transcriptome # |
|---|---|---|
| Raw Data | ||
| Raw sequencing reads | 456,775,568 | 122,806,922 |
| Clean reads | 412,914,751 | 111,524,231 |
| Contig statistics | ||
| Number of contigs | 90,290 | 245,053 |
| Total contig size, Mb | 640.1 | 278.5 |
| Contig N50 size, bp | 10,878 | 1760 |
| Longest contig, bp | 87,474 | 15,773 |
| GC/AT/N, % | 44.45 | 48.10 |
| Scaffold statistics | ||
| Number of scaffolds | 45,321 | - |
| Total scaffold size, Mb | 641.5 | - |
| Scaffold N50 size, bp | 25,577 | - |
| Longest scaffold, bp | 285,113 | - |
| Genome coverage, × | 59 | - |
|
BUSCO Completeness
(Met/Ver/Actino) |
||
| Complete, % | 82.7/70.5/68.8 | 99.1/80.6/72 |
| Complete and single copy, % | 78.8/68.4/66.3 | 41.5/31.2/29.1 |
| Complete and duplicated, % | 3.9/2.1/2.5 | 57.6/49.4/42.9 |
| Fragmented, % | 9.2/19.0/13.3 | 0.6/10.5/8.6 |
| Missing, % | 8.1/10.5/17.9 | 0.3/8.9/19.4 |
| Total BUSCO found | 91.9/89.5/82.1 | 99.7/91.1/80.6 |
| Annotation | ||
| Number of protein-coding genes | 29,701 | - |
| Number of functionally annotated proteins | 28,783 | - |
| Average CDS length | 1561.42 | - |
| Longest CDS | 49,643 | - |
| Average protein length | 373.45 | - |
| Longest protein | 16,525 | - |
| Average number of exon per gene | 6.59 | - |
# All statistics are based on contigs/scaffolds of size ≥200 bp. Met: From a total of 978 genes of Metazoa library profile; Ver: From a total of 2586 genes of Vertebrata library profile; Actino: From a total of 4584 genes of Actinopterygii library profile.