Data from: Looking into the past – the reaction of three grouse species to climate change over the last million years using whole genome sequences

Kozma R, Melsted P, Magnússon KP, Höglund J

Date Published: November 24, 2015

DOI: http://dx.doi.org/10.5061/dryad.11p3v

 

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Title Willow grouse autosomal consensus sequence
Downloaded 20 times
Description Willow grouse autosomal 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 (22) and maximum read depth (-D) set to twice the mean genome coverage (136)). All non-autosomal sites were discarded.
Download L.lago.autosomes.fq.gz (336.1 Mb)
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Title Rock ptarmigan autosomal consensus sequence
Downloaded 16 times
Description Rock ptarmigan autosomal 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 (33) and maximum read depth (-D) set to twice the mean genome coverage (202)). All non-autosomal sites were discarded.
Download L.muta.autosomes.fq.gz (319.8 Mb)
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Title Black grouse autosome consensus sequence
Downloaded 16 times
Description 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.
Download T.tetrix.autosomes.fq.gz (371.9 Mb)
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Title LastZ output files
Downloaded 17 times
Description 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.
Download LastZ.zip (25.86 Mb)
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Title Willow grouse autosomal heterozygous sites
Downloaded 12 times
Description A vcf file containing the autosomal heterozygous sites of the willow grouse individual. It was generated by the default samtools mpileup and bcftools pipeline. Filtering was performed by vcffilter (from the vcflib suite: https://github.com/ekg/vcflib) to keep only heterozygous sites with read depth between 22 and 136 and mapping quality above 20. Indels were removed by vcftools (v0.1.13), using the '--remove-indels' function.
Download L.lago.auto.het.vcf.gz (71.23 Mb)
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Title Rock ptarmigan autosomal heterozygous sites
Downloaded 9 times
Description A vcf file containing the autosomal heterozygous sites of the rock ptarmigan individual. It was generated by the default samtools mpileup and bcftools pipeline. Filtering was performed by vcffilter (from the vcflib suite: https://github.com/ekg/vcflib) to keep only heterozygous sites with read depth between 33 and 202 and mapping quality above 20. Indels were removed by vcftools (v0.1.13), using the '--remove-indels' function.
Download L.muta.auto.het.vcf.gz (42.91 Mb)
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Title Black grouse autosomal heterozygous sites
Downloaded 13 times
Description A vcf file containing the autosomal heterozygous sites of the black grouse individual. It was generated by the default samtools mpileup and bcftools pipeline. Filtering was performed by vcffilter (from the vcflib suite: https://github.com/ekg/vcflib) to keep only heterozygous sites with read depth between 28 and 171 and mapping quality above 20. Indels were removed by vcftools (v0.1.13), using the '--remove-indels' function.
Download T.tetrix.auto.het.vcf.gz (20.73 Mb)
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When using this data, please cite the original publication:

Kozma R, Melsted P, Magnússon KP, Höglund J (2016) Looking into the past – the reaction of three grouse species to climate change over the last million years using whole genome sequences. Molecular Ecology, 25(2): 570–580. http://dx.doi.org/10.1111/mec.13496

Additionally, please cite the Dryad data package:

Kozma R, Melsted P, Magnússon KP, Höglund J (2015) Data from: Looking into the past – the reaction of three grouse species to climate change over the last million years using whole genome sequences. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.11p3v
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