I'd like to ask about the meaning of the 5th column (an integer number) in BED format results from repeatmasker.
9 100663131 100663387 LTR22_SS 475 +
9 70254161 70254685 ALTR2B_SSc 3460 +
9 96468811 96469391 LTR8_SSc 3756 -
9 116391614 116392469 LTR78 1152 +
9 4980341 4980930 LTR39_SSc 3300 -
9 16908116 16908359 MamGypLTR3 512 +
9 17432426 17432886 ALTR2B2_SSc 1914 -
9 18742941 18743430 LTR5_SS 2771 +
9 27131556 27132076 ERV3-1_SSc-LTR 969 -
9 30539515 30539909 LTR39B3_SSc 787 -
Searched around but did not find a definite answer, so seeking help here from repeatmasker experts. It is clearly not length of the repeat. Is it something indicating how repetitive this feature is in the genome? Or some identity scores indicating its match to some sort of repeat consensus?
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Vitis
1 answer
It is the Smith-Waterman alignment score of matches with coding sequence.
I think (but am not 100% certain) a higher score means greater similarity with coding sequence, indicating a less repetitive region. It is used for cutoff filters, which are specific to different classes of repeats.
I don't know how useful it is to use these scores directly. Also see "How to read the results" from the Repeatmasker documentation:
Smith-Waterman score of the match, usually complexity adjusted The SW scores are not always directly comparable. Sometimes the complexity adjustment has been turned off, and a variety of scoring-matrices are used.
It may be worthwhile to contact the developers directly.
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Column 5 is an optional field for BED files. The description of field 5 is below, from UCSC
You may have already known that... Not sure how they determine the scores here, sorry.