Genomic resequencing data in the northern bottlenose whale, Hyperoodon ampullatus
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...
Main Authors: | , , , , , , , , |
---|---|
Format: | Other/Unknown Material |
Language: | unknown |
Published: |
Zenodo
2022
|
Subjects: | |
Online Access: | https://doi.org/10.5281/zenodo.6640042 |
id |
ftzenodo:oai:zenodo.org:6640042 |
---|---|
record_format |
openpolar |
spelling |
ftzenodo:oai:zenodo.org:6640042 2024-09-15T18:11:18+00:00 Genomic resequencing data in the northern bottlenose whale, Hyperoodon ampullatus de Greef, Evelien Einfeldt, Anthony Miller, Patrick Ferguson, Steve Garroway, Colin Lefort, Kyle Paterson, Ian Bentzen, Paul Feyrer, Laura 2022-06-13 https://doi.org/10.5281/zenodo.6640042 unknown Zenodo https://doi.org/10.5281/zenodo.4541510 https://doi.org/10.5281/zenodo.6640042 oai:zenodo.org:6640042 info:eu-repo/semantics/openAccess Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode info:eu-repo/semantics/other 2022 ftzenodo https://doi.org/10.5281/zenodo.664004210.5281/zenodo.4541510 2024-07-26T14:36:29Z 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), biallelic sites, autosomes, removed structural variants, minor allele count 2, minimum scaffold length 50kb, and sites in Hardy-Weinberg Equilibrium 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, biallelic sites, autosomes, removed structural variants, minimum scaffold length 100kb, and sites in Hardy-Weinberg Equilibrium NBW_SNPS_filtered_imputed_haplotype_analyses.vcf.gz - Filtered and imputed SNPs for haplotype analyses. Filtered for quality, biallelic sites, autosomes, removed 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, removed structural variants, minor allele count 2, minimum scaffold length 50kb. Other/Unknown Material hyperoodon ampullatus Northern bottlenose whale Zenodo |
institution |
Open Polar |
collection |
Zenodo |
op_collection_id |
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), biallelic sites, autosomes, removed structural variants, minor allele count 2, minimum scaffold length 50kb, and sites in Hardy-Weinberg Equilibrium 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, biallelic sites, autosomes, removed structural variants, minimum scaffold length 100kb, and sites in Hardy-Weinberg Equilibrium NBW_SNPS_filtered_imputed_haplotype_analyses.vcf.gz - Filtered and imputed SNPs for haplotype analyses. Filtered for quality, biallelic sites, autosomes, removed 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, removed 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 Genomic resequencing data in the northern bottlenose whale, Hyperoodon ampullatus |
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 |
Genomic resequencing data in the northern bottlenose whale, Hyperoodon ampullatus |
title_short |
Genomic resequencing data in the northern bottlenose whale, Hyperoodon ampullatus |
title_full |
Genomic resequencing data in the northern bottlenose whale, Hyperoodon ampullatus |
title_fullStr |
Genomic resequencing data in the northern bottlenose whale, Hyperoodon ampullatus |
title_full_unstemmed |
Genomic resequencing data in the northern bottlenose whale, Hyperoodon ampullatus |
title_sort |
genomic resequencing data in the northern bottlenose whale, hyperoodon ampullatus |
publisher |
Zenodo |
publishDate |
2022 |
url |
https://doi.org/10.5281/zenodo.6640042 |
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.6640042 oai:zenodo.org:6640042 |
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.664004210.5281/zenodo.4541510 |
_version_ |
1810448880410558464 |