Schema for LTRharvest - LTR Fragments Identified by LTRharvest
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Database: DmojImproved Primary Table: ltrharvest_LTR_retrotransposon Row Count: 4,067
field | example | SQL type | info |
bin | 585 | smallint(5) unsigned | range |
chrom | improved_6498 | varchar(255) | values |
chromStart | 547 | int(10) unsigned | range |
chromEnd | 15515 | int(10) unsigned | range |
name | LTR_retrotransposon1 | varchar(255) | values |
score | 1000 | int(10) unsigned | range |
strand | + | char(1) | values |
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Sample Rows
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bin | chrom | chromStart | chromEnd | name | score | strand |
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585 | improved_6498 | 547 | 15515 | LTR_retrotransposon1 | 1000 | + |
585 | improved_6498 | 55758 | 59761 | LTR_retrotransposon2 | 1000 | - |
585 | improved_6498 | 74781 | 87475 | LTR_retrotransposon3 | 1000 | - |
585 | improved_6498 | 88508 | 99923 | LTR_retrotransposon4 | 1000 | + |
585 | improved_6498 | 101068 | 110690 | LTR_retrotransposon5 | 1000 | - |
585 | improved_6498 | 121042 | 123720 | LTR_retrotransposon6 | 1000 | + |
586 | improved_6498 | 138776 | 144830 | LTR_retrotransposon7 | 1000 | - |
586 | improved_6498 | 156890 | 171308 | LTR_retrotransposon8 | 1000 | - |
586 | improved_6498 | 176547 | 182377 | LTR_retrotransposon9 | 1000 | - |
586 | improved_6498 | 186676 | 191742 | LTR_retrotransposon10 | 1000 | - |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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LTRharvest (ltr_harvest) Track Description
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Description
LTRharvest
is used to identify putative long terminal repeats (LTR)
retrotransposons in the D. mojavensis genome using the following parameters:
- -mintsd 4
- -maxtsd 20
- -minlenltr 100
- -maxlenltr 1000
- -mindistltr 1000
- -maxdistltr 15000
Additional features within the LTR retrotransposons are annotated using
LTRdigest.
References
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