Black grouse autosome consensus sequence

Black grouse autosome consensus sequence used as input for PSMC. The file was generated from a filtered bam file using the samtools mpileup, bcftools and vcfutils.pl (vcf2fq) pipeline (downgrading mapping quality for reads containing excessive mismatches (-C) to 50, minimum read depth (-d) set to 1/...

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Bibliographic Details
Main Authors: Kozma, Radoslav, Melsted, Páll, Magnússon, Kristinn P., Höglund, Jacob
Format: Dataset
Language:unknown
Published: Dryad Digital Repository 2015
Subjects:
Effective population size
Climate hange
PSMC
Holarctic
Pleistocene
Holocene
Tetrao tetrix
Lagopus lagopus
Lagopus muta
Tetraoninae
Online Access:https://dx.doi.org/10.5061/dryad.11p3v/3
http://datadryad.org/resource/doi:10.5061/dryad.11p3v/3
Description
Summary:Black grouse autosome consensus sequence used as input for PSMC. The file was generated from a filtered bam file using the samtools mpileup, bcftools and vcfutils.pl (vcf2fq) pipeline (downgrading mapping quality for reads containing excessive mismatches (-C) to 50, minimum read depth (-d) set to 1/3 of the mean genome coverage (28) and maximum read depth (-D) set to twice the mean genome coverage (171)). All non-autosomal sites were discarded.

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