Data from: Population connectivity and genetic structure of burbot (Lota lota) populations in the Wind River Basin, Wyoming

Underwood ZE, Mandeville EG, Walters AW

Date Published: October 16, 2015

DOI: http://dx.doi.org/10.5061/dryad.7842r

 

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Title VCF file
Downloaded 9 times
Description This is a .vcf file produced by calling variant genetic sites using samtools and bcftools. For each variant site identified, we required that >60% of all individuals had 1 or more read at that locus.
Download variants_0.6.vcf (69.02 Mb)
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Title entropy_variants0.6
Downloaded 4 times
Description Input file for analysis with the "entropy" model. This file is a filtered version of the VCF file, including genotype likelihoods for loci with MAF>1%. Additionally, we randomly selected 1 SNP per contig for contigs with multiple variant sites, to ensure independence of SNPs.
Download entropy_variants0.6.mpgl (17.35 Mb)
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Title split_scaffold_burbot_ref_long_94
Downloaded 5 times
Description Because there are no existing genomic resources for burbot, we constructed an artificial reference genome using smng (Seq- Man NGen, DNAstar), using 25 million reads. This artificial reference genome contains 53,789 contigs. We used this assembly as a template to for a reference-based assembly with bwa.
Download split_scaffold_burbot_ref_long_94.fasta (5.576 Mb)
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When using this data, please cite the original publication:

Underwood ZE, Mandeville EG, Walters AW (2015) Population connectivity and genetic structure of burbot (Lota lota) populations in the Wind River Basin, Wyoming. Hydrobiologia 765(1): 329-342. http://dx.doi.org/10.1007/s10750-015-2422-y

Additionally, please cite the Dryad data package:

Underwood ZE, Mandeville EG, Walters AW (2015) Data from: Population connectivity and genetic structure of burbot (Lota lota) populations in the Wind River Basin, Wyoming. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.7842r
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