The meaning of "perc div" in genome.out in main output dir

[Zhenlisme]

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]

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.