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rmhubley / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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The meaning of "perc div" in genome.out in main output dir #216

Open Zhenlisme opened 1 year ago

Zhenlisme commented 1 year ago

Hello,

Could you please give me more information about the meaning of "perc div" column in genome.out file? Is it just as same as the Kimura% ?

Thank you for your help. Best ragards, Zhen

rmhubley commented 11 months ago

The standard .out file format is based on Phil Green's crossmatch output. The 'perc div' is simply the percent substitution ( aligned_mismatched_bases / total_aligned_bases ). The .align files have Kimura divergence calculated in the stanza following each alignment.