Table 1 Completeness of major versions of assembled and annotated genome of Grapholita molesta estimated by BUSCO.
From: Population genomic signatures of the oriental fruit moth related to the Pleistocene climates
Step | Version | Software | Complete % | Single copy % | Duplication % | Fragment % | Missing % | Size (Mb)/No. gene | N50 (Mb) |
|---|---|---|---|---|---|---|---|---|---|
Assembly | Contig assembly | CANU | 83.3 | 57.7 | 25.6 | 7.1 | 9.6 | 949.05 | 0.85 |
Synteny reduction | purge_haplogs | 76.6 | 74.7 | 1.9 | 10.5 | 12.9 | 521.60 | 1.79 | |
Contig polish | PILON | 96.7 | 93.1 | 3.6 | 1.1 | 2.2 | 524.93 | 1.79 | |
Linkage group assembly | Juicer + 3D-DNA | 93.3 | 92.2 | 1.1 | 1.0 | 5.7 | 525.22 | 19.5 | |
Linkage group polish | PILON | 97.1 | 96.1 | 1.0 | 1.0 | 1.9 | 517.71 | 19.5 | |
Annotation | Annotation | MAKER | 90.1 | 86.1 | 4.0 | 6.6 | 3.3 | 39,274 | NA |
Filtering based on expression | In-home script | 89.8 | 85.9 | 3.9 | 6.1 | 4.1 | 19,478 | NA | |
Gene structure improvement | PASA | 92.6 | 76.6 | 16.0 | 4.4 | 3.0 | 19,968 | NA | |
Functional annotation | EGGNOG | 92.6 | 76.6 | 16.0 | 4.3 | 3.1 | 15,269 | NA |
