Repeat annotation of Linum tenue
Description
The file contains the annotation for the repetitive regions in
Linum tenue
.
The detection of repeats has been done with RepeatMasker/RepeatModeler (https://www.repeatmasker.org/) using a custom repeat library.
The genome has been deposited to ENA with the accession id: GCA_946122785 (Project PRJEB52918). See link below.
It is part of this article Gutiérrez-Valencia, J., Fracassetti, M., Berdan, E. L., Bunikis, I., Soler, L., Dainat, J., ... & Slotte, T. (2022). Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level.
Current Biology
,
32
(20), 4360-4371. 10.1016/j.cub.2022.08.042
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-24343000 |
Tags
- dataset
- evolutionary-ecology