LastZ output files

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, --gapp...

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Bibliographic Details
Main Authors: Kozma, Radoslav, Melsted, Páll, Magnússon, Kristinn P., Höglund, Jacob
Format: Dataset
Language:unknown
Published: 2015
Subjects:
Effective population size
Climate hange
PSMC
rock ptarmigan
Online Access:http://hdl.handle.net/10255/dryad.102499
https://doi.org/10.5061/dryad.11p3v/4
Description
Summary: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.

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