Evaluating population structure in the northern bottlenose whale, Hyperoodon ampullatus, using genomic resequencing data
This dataset contains resequencing data used in our northern bottlenose whale genomics research. In this project, we analyzed population structure, demographic history, and signatures of selection.Source code for genomic analyses is available at github.com/edegreef/NBW-resequencing . Data uploaded h...
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ftzenodo:oai:zenodo.org:5719248 2024-09-15T18:11:18+00:00 Evaluating population structure in the northern bottlenose whale, Hyperoodon ampullatus, using genomic resequencing data de Greef, Evelien Einfeldt, Anthony Miller, Patrick Ferguson, Steve Garroway, Colin Lefort, Kyle Paterson, Ian Bentzen, Paul Feyrer, Laura 2021-12-09 https://doi.org/10.5281/zenodo.5719248 unknown Zenodo https://doi.org/10.5281/zenodo.4541510 https://doi.org/10.5281/zenodo.5719248 oai:zenodo.org:5719248 info:eu-repo/semantics/openAccess Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode info:eu-repo/semantics/other 2021 ftzenodo https://doi.org/10.5281/zenodo.571924810.5281/zenodo.4541510 2024-07-27T07:23:29Z This dataset contains resequencing data used in our northern bottlenose whale genomics research. In this project, we analyzed population structure, demographic history, and signatures of selection.Source code for genomic analyses is available at github.com/edegreef/NBW-resequencing . Data uploaded here contain: NBW_all_variantcalls.vcf.gz - All variant calls, including both indels and SNPs NBW_SNPS_unfiltered.vcf.gz - Unfiltered SNPs NBW_SNPS_filtered_population_analyses.vcf.gz -Filtered SNPs for population analyses. Filtered for quality (removed qual < 20, mq < 30, qd < 2, missingness > 0.4), non-biallelic sites, autosomes, structural variants, minor allele count 2, minimum scaffold length 50kb NBW_SNPS_filtered_pruned_population_analyses.vcf.gz - Additionally LD-pruned with r2> 0.5 NBW_SNPS_filtered_demography_analyses.vcf.gz - Filtered SNPs for demography analyses. Filtered for quality, non-biallelic sites, autosomes, structural variants, minimum scaffold length 100kb. NBW_SNPS_filtered_imputed_haplotype_analyses.vcf.gz - Filtered and imputed SNPs for haplotype analyses. Filtered for quality, non-biallelic sites, autosomes, structural variants, max-missingness 0.1, minor allele count 2, minimum scaffold length 50kb. NBW_SNPS_filtered_Xchr.vcf.gz & NBW_SNPS_filtered_Ychr_males.vcf.gz - Filtered SNPs on X & Y chr. Filtered for quality, non-biallelic sites, structural variants, minor allele count 2, minimum scaffold length 50kb. Other/Unknown Material hyperoodon ampullatus Northern bottlenose whale Zenodo |
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Open Polar |
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ftzenodo |
language |
unknown |
description |
This dataset contains resequencing data used in our northern bottlenose whale genomics research. In this project, we analyzed population structure, demographic history, and signatures of selection.Source code for genomic analyses is available at github.com/edegreef/NBW-resequencing . Data uploaded here contain: NBW_all_variantcalls.vcf.gz - All variant calls, including both indels and SNPs NBW_SNPS_unfiltered.vcf.gz - Unfiltered SNPs NBW_SNPS_filtered_population_analyses.vcf.gz -Filtered SNPs for population analyses. Filtered for quality (removed qual < 20, mq < 30, qd < 2, missingness > 0.4), non-biallelic sites, autosomes, structural variants, minor allele count 2, minimum scaffold length 50kb NBW_SNPS_filtered_pruned_population_analyses.vcf.gz - Additionally LD-pruned with r2> 0.5 NBW_SNPS_filtered_demography_analyses.vcf.gz - Filtered SNPs for demography analyses. Filtered for quality, non-biallelic sites, autosomes, structural variants, minimum scaffold length 100kb. NBW_SNPS_filtered_imputed_haplotype_analyses.vcf.gz - Filtered and imputed SNPs for haplotype analyses. Filtered for quality, non-biallelic sites, autosomes, structural variants, max-missingness 0.1, minor allele count 2, minimum scaffold length 50kb. NBW_SNPS_filtered_Xchr.vcf.gz & NBW_SNPS_filtered_Ychr_males.vcf.gz - Filtered SNPs on X & Y chr. Filtered for quality, non-biallelic sites, structural variants, minor allele count 2, minimum scaffold length 50kb. |
format |
Other/Unknown Material |
author |
de Greef, Evelien Einfeldt, Anthony Miller, Patrick Ferguson, Steve Garroway, Colin Lefort, Kyle Paterson, Ian Bentzen, Paul Feyrer, Laura |
spellingShingle |
de Greef, Evelien Einfeldt, Anthony Miller, Patrick Ferguson, Steve Garroway, Colin Lefort, Kyle Paterson, Ian Bentzen, Paul Feyrer, Laura Evaluating population structure in the northern bottlenose whale, Hyperoodon ampullatus, using genomic resequencing data |
author_facet |
de Greef, Evelien Einfeldt, Anthony Miller, Patrick Ferguson, Steve Garroway, Colin Lefort, Kyle Paterson, Ian Bentzen, Paul Feyrer, Laura |
author_sort |
de Greef, Evelien |
title |
Evaluating population structure in the northern bottlenose whale, Hyperoodon ampullatus, using genomic resequencing data |
title_short |
Evaluating population structure in the northern bottlenose whale, Hyperoodon ampullatus, using genomic resequencing data |
title_full |
Evaluating population structure in the northern bottlenose whale, Hyperoodon ampullatus, using genomic resequencing data |
title_fullStr |
Evaluating population structure in the northern bottlenose whale, Hyperoodon ampullatus, using genomic resequencing data |
title_full_unstemmed |
Evaluating population structure in the northern bottlenose whale, Hyperoodon ampullatus, using genomic resequencing data |
title_sort |
evaluating population structure in the northern bottlenose whale, hyperoodon ampullatus, using genomic resequencing data |
publisher |
Zenodo |
publishDate |
2021 |
url |
https://doi.org/10.5281/zenodo.5719248 |
genre |
hyperoodon ampullatus Northern bottlenose whale |
genre_facet |
hyperoodon ampullatus Northern bottlenose whale |
op_relation |
https://doi.org/10.5281/zenodo.4541510 https://doi.org/10.5281/zenodo.5719248 oai:zenodo.org:5719248 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode |
op_doi |
https://doi.org/10.5281/zenodo.571924810.5281/zenodo.4541510 |
_version_ |
1810448879706963968 |