LastZ output files
2016-11-02T12:48:41Z (GMT) by
LastZ output files for the alignment of each autosome of each grouse species and its respective chicken chromosome. Gg - chicken, Ll - willow grouse, Lm - rock ptarmigan and Tt - black grouse. Each LastZ (v1.03.54) run was applied with the following parameters: --ydrop=9400, --hspthresh=4500, --gappedthresh=3000 and –notransition. The 'nmatch' and 'nmismatch' columns (7 and 8 respectively in the output files) were used to calculate the mutation rate according to the formula: (sum of mismatches / [sum of matches + mismatches]) / 2x41.88; where 41.88 is the divergence time (million years) between chicken and the three grouse species.