| Analysis Name | Solanum pinnatisectum 'LQN (Isolate)' ASM3557808v1 Assembly & Annotation |
| Sequencing technology | Oxford Nanopore PromethION |
| Assembly method | NextDenovo v. 2.5.2 |
| Release Date | 2024-01-12 |
No publication. NCBI BioProject PRJNA1030533. Solanum Pinnatisectum Genome sequencing.
Assembly statistics
| Genome size | 664.1 Mb |
| Number of chromosomes | 12 |
| Number of scaffolds | 140 |
| Scaffold N50 | 49.2 Mb |
| Scaffold L50 | 6 |
| Number of contigs | 339 |
| Contig N50 | 9.1 Mb |
| Contig L50 | 20 |
| Assembly level | Chromosome |
The Solanum pinnatisectum 'LQN (Isolate)' ASM3557808v1 assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GCA_035578085.1_ASM3557808v1_genomic.fna.gz |
The Solanum pinnatisectum 'LQN (Isolate)' ASM3557808v1 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | GCA_035578085.1_ASM3557808v1_genomic.gff.gz |
| CDS sequences (FASTA file) | GCA_035578085.1_ASM3557808v1_translated_cds.faa.gz |
| Protein sequences (FASTA file) | GCA_035578085.1_ASM3557808v1_protein.faa.gz |
Functional annotation for the Solanum pinnatisectum 'LQN (Isolate)' ASM3557808v1 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Solanum_pinnatisectum_LQN_ASM3557808v1.Pfam.tsv.gz |
Summary
| Query | Chr | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| SLF15 | CM069076.1 | 68,988,332 | 3033868-3032609 | Solanum tuberosum DM8.1, SLF15 | 96.4 | F-box domain |
| SLF15-2Ψ | CM069076.1 | 68,988,332 | 3101363-3100112 | Solanum tuberosum DM8.1, SLF15 | 95.9 | - |
| SLF16Ψ | CM069076.1 | 68,988,332 | 4158467-4157287 | Solanum tuberosum DM8.1, SLF16 | 97.6 | - |
| SLF6Ψ | CM069076.1 | 68,988,332 | 21244843-21245991 | Solanum tuberosum DM8.1, SLF6-2 | 95.1 | - |
| SLF9 | CM069076.1 | 68,988,332 | 24759940-24761025 | Solanum tuberosum DM8.1, SLF9 | 97.4 | F-box domain |
| SLF4Ψ | CM069076.1 | 68,988,332 | 26314375-26313210 | Solanum pimpinellifolium KJ814871.1, SLF4 | 92.8 | - |
| SLF18 | CM069076.1 | 68,988,332 | 40526508-40527620 | Solanum tuberosum DM8.1, SLF18 | 95.4 | F-box domain |
Nucleotide
Protein