Repeat annotation of Linum trigynum
Description
The file contains the annotation fo the repetitive regions in *Linum trigynum*.
The detection of Repeat has been done with [RepeatMasker/RepeatModeler](https://www.repeatmasker.org/) using a custom repeat library.
The genome has been deposited to [ENA](https://www.ebi.ac.uk/ena/browser/home) with the accession id: GCA_964030455 (project PRJEB67577).
It is part of this article: Gutiérrez-Valencia, J., Zervakis, P. I., Postel, Z., Fracassetti, M., Losvik, A., Mehrabi, S., ... & Slotte, T. (2024). Genetic causes and genomic consequences of breakdown of distyly in Linum trigynum. Molecular Biology and Evolution, msae087. https://doi.org/10.1093/molbev/msae087
The file is in BED format converted with [BEDOPS](https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/rmsk2bed.html). The fourth (Repeat class) and eleventh (Repeat name) columns have been reversed to highlight the Repeat name in the visualization.
Query sequence 1 chromosome
Query start 2 start
Query end 3 stop
Repeat class 4 id
Smith-Waterman score 5 score
Strand 6 strand
Percentage, substitutions 7
Percentage, deleted bases 8
Percentage, inserted bases 9
Bases in query, past match 10
Repeat name 11
Bases in complement of the repeat consensus sequence 12
Match start 13
Match end 14
Unique ID 15
Higher-scoring match (optional) 16
Resources
| Name |
Format |
Description |
Link |
|
0 |
|
http://data.europa.eu/88u/dataset/https-doi-org-10-17044-scilifelab-24324310 |
Tags
- dataset
- evolutionary-ecology