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113 results for “VCF”
Chromosome VCF files and 1Mb recombination rate estimations for: Fine-scale recombination rate variation and association with genomic features in a butterfly
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Populations genomics of deep-sea hydrothermal vent copepod Stygiopontius lauensis: from raw fasta files to filtered vcf file
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VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species
<p>Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a "protracted period" of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.</p>
VCF file of multiple single-cyst-derived Ro1 and Ro2 lines of New York fields on Globodera rostochiensis genome
<p>The potato cyst nematode, <em>Globodera rostochiensis</em>, is a regulated pest posing a serious threat to potato production worldwide. Although the endemic pathotype (Ro1) of <em>G. rostochiensis</em> has been confined to New York State for several decades as a result of quarantine regulations and management with resistant potato cultivars, a virulent pathotype, Ro2, has emerged, for which control measures are scarce. The ability to detect Ro2 early in fields is necessary to sustain the success of <em>G. rostochiensis</em> quarantine in the US. Here, we report the comparative analysis of whole-genome sequences of multiple single-cyst-derived Ro1 and Ro2 lines, propagated from original field populations. The identified discriminant variants are good targets for developing molecular diagnostic tools for differentiating <em>G. rostochiensis</em> pathotypes in NY.</p>
Reference flow VCF for pre-built genomes
<p>Pre-built genomes (in VCF format) for the RandFlow-LD and RandFlow-LD-26 methods in reference flow. The references can be built using the reference flow software (https://github.com/langmead-lab/reference_flow). An archival version of the software is available at http://doi.org/10.5281/zenodo.4287778</p> <p> </p> <p>The reference flow method is described at https://www.biorxiv.org/content/10.1101/2020.03.03.975219v4</p>
VCF data file and code for: CYP2J19 mediates carotenoid colour introgression across a natural avian hybrid zone
<p><span>It has long been of interest to identify the phenotypic traits that mediate reproductive isolation between related species, and more recently, the genes that underpin them. Much work has focused on identifying genes associated with animal colour, with the candidate gene <i>CYP2J19</i> identified in laboratory studies as the ketolase converting yellow dietary carotenoids to red ketocarotenoids in birds with red pigments. But evidence that <i>CYP2J19</i> explains variation between red and yellow feather coloration in wild populations of birds is lacking. Hybrid zones provide the opportunity to identify genes associated with specific traits. Here we investigate genomic regions associated with colour in red-fronted and yellow-fronted tinkerbirds across a hybrid zone in southern Africa. We sampled 85 individuals, measuring spectral reflectance of forecrown feathers and scoring colours from photographs, while testing for carotenoid presence with Raman spectroscopy. We performed a genome-wide association study to identify associations with carotenoid-based coloration, using double-digest RAD sequencing aligned to a short-read whole genome of a <i>Pogoniulus</i> tinkerbird. Admixture mapping using 104,933 SNPs identified a region of chromosome 8 that includes <i>CYP2J19</i> as the only locus with more than two SNPs significantly associated with both crown hue and crown score, while Raman spectra provided evidence of ketocarotenoids in red feathers. Asymmetric backcrossing in the hybrid zone suggests that yellow-fronted females mate more often with red-fronted males than vice versa. Female red-fronted tinkerbirds mating assortatively with red-crowned males is consistent with the hypothesis that converted carotenoids are an honest signal of quality.</span></p>
Phased VCF outputs for "HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing"
<p>The collection of raw and processed VCF files for the paper titled: "HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing".</p><p>Raw VCF files from DeepVariant, pbsv, and TRGT are included in the unphased subfolder. Outputs from WhatsHap and HiPhase are in their own subfolders. Three replicates of HG002 are included in all subfolders. Layout is as follows:</p><blockquote><p>hiphase_vcfs</p><p>├── all_vcfs.md5</p><p>├── hiphase</p><p>│ ├── HG002-rep1.GRCh38.deepvariant.hiphase.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.deepvariant.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep1.GRCh38.pbsv.hiphase.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.pbsv.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep1.GRCh38.trgt.hiphase.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.trgt.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.deepvariant.hiphase.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.deepvariant.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.pbsv.hiphase.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.pbsv.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.trgt.hiphase.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.trgt.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.deepvariant.hiphase.vcf.gz</p><p>│ ├── HG002-rep3.GRCh38.deepvariant.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.pbsv.hiphase.vcf.gz</p><p>│ ├── HG002-rep3.GRCh38.pbsv.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.trgt.hiphase.vcf.gz</p><p>│ └── HG002-rep3.GRCh38.trgt.hiphase.vcf.gz.tbi</p><p>├── unphased</p><p>│ ├── HG002-rep1.GRCh38.deepvariant.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.deepvariant.vcf.gz.tbi</p><p>│ ├── HG002-rep1.GRCh38.pbsv.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.pbsv.vcf.gz.tbi</p><p>│ ├── HG002-rep1.GRCh38.trgt.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.trgt.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.deepvariant.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.deepvariant.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.pbsv.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.pbsv.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.trgt.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.trgt.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.deepvariant.vcf.gz</p><p>│ ├── HG002-rep3.GRCh38.deepvariant.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.pbsv.vcf.gz</p><p>│ ├── HG002-rep3.GRCh38.pbsv.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.trgt.vcf.gz</p><p>│ └── HG002-rep3.GRCh38.trgt.vcf.gz.tbi</p><p>└── whatshap</p><p> ├── HG002-rep1.GRCh38.deepvariant.whatshap.vcf.gz</p><p> ├── HG002-rep1.GRCh38.deepvariant.whatshap.vcf.gz.tbi</p><p> ├── HG002-rep2.GRCh38.deepvariant.whatshap.vcf.gz</p><p> ├── HG002-rep2.GRCh38.deepvariant.whatshap.vcf.gz.tbi</p><p> ├── HG002-rep3.GRCh38.deepvariant.whatshap.vcf.gz</p><p> └── HG002-rep3.GRCh38.deepvariant.whatshap.vcf.gz.tbi</p><p>3 directories, 43 files</p></blockquote>
VCF file of whole genome sequencing data of 163 rats mapped jointly to mRatBN7.2
<p>We analyzed whole genome sequencing data of 163 rats. These data were first mapped to mRatBN7.2, followed by variant calling using deepvariant and joint analysis using GLNexus. Sites that are likely called due to base-level errors in mRatBN7.2 are removed. </p>
Obovaria olivaria maf filtered vcf file from: RAD-tag and mitochondrial DNA sequencing reveal the genetic structure of a widespread and regionally imperiled freshwater mussel, Obovaria olivaria (Bivalvia: Unionidae)
<p><em>Obovaria olivaria</em> is a species of freshwater mussel native to the Mississippi River and Laurentian Great Lakes-St. Lawrence River drainages of North America. This mussel has experienced population declines across large parts of its distribution and is imperiled in many jurisdictions. <em>Obovaria olivaria </em>uses the similarly imperiled <em>Acipenser fulvescens</em> (Lake Sturgeon) as a host for its glochidia. We employed mitochondrial DNA sequencing and Restriction-site Associated DNA sequencing (RAD-seq) to assess patterns of genetic diversity and population structure of <em>O. olivaria</em> from 19 collection locations including the St. Lawrence River drainage, the Great Lakes drainage, the Upper Mississippi River drainage, the Ohioan River drainage and the Mississippi Embayment. Heterozygosity was highest in Upper Mississippi and Great Lakes populations, followed by a reduction in diversity and relative effective population size in the St. Lawrence populations. Pairwise <em>F</em><sub>ST</sub> ranged from 0.00 to 0.20, and analyses of genetic structure revealed two major ancestral populations, one including all St. Lawrence River/Ottawa River sites and the other including remaining sites; however, significant admixture and isolation by river distance across the range were evident. The genetic diversity and structure of <em>O. olivaria</em> is consistent with the existing literature on <em>Acipenser fulvescens</em> and suggest that, although northern and southern <em>O. olivaria</em> populations are genetically distinct, genetic structure in <em>O. olivaria</em> is largely clinal rather than discrete across its range. Conservation and restoration efforts of <em>O. olivaria</em> should prioritize the maintenance and restoration of locations where <em>O. olivaria </em>remain, especially in northern rivers, and to ensure connectivity that will facilitate dispersal of <em>Acipenser fulvescens</em> and movement of encysted glochidia.</p>
VCF for neutral data set in Harpagifer bispinis along the Magellan Province
<p>Quaternary glacial cycles shaped the current distribution of polar and cold-temperate biotas. In the Magellan province of South America, ice covering during the last glacial maximum radically altered the landscape/seascape, speciation rate, and the distribution of species. Here we studied nototheniid fishes <i>Harpagifer </i>spp. along the Magellan province reported as two nominal species: <i>H. bispinis</i> in Patagonia and <i>H. palliolatus</i>, endemic to the Falkland/Malvinas Islands. Previous molecular analyses in <i>Harpagifer</i> showed that the genus may have recently colonized southern South America ~ 1 million years ago. The extensive use in systematics of molecular markers to determine evolutionary units has been improved due to the advances in NGS. Combining traditional DNA sequences and non-targeted GBS-SNPs we evaluated both, the presence of effective evolutionary units and contemporary patterns of genetic structure across the Magellan province. DNA sequences consistently showed an absence of phylogeographic structure, with shared dominant haplotypes between nominal species, pointing towards the presence of a single evolutionary unit. In contrast, SNPs identified three groups in Patagonia, two located north and south of the Strait of Magellan, and a third well-differentiated one in the Falkland/Malvinas Islands. Connectivity analyses using SNPs suggest limited and asymmetric gene flow from Patagonia to the Falkland/Malvinas. Contrasting rough- and fine-scale genetic evolutionary patterns recorded in <i>Harpagifer</i> enhance the relevance in the use of combined methodologies for species delimitation analyses. Depending on the question to be addressed, we could discriminate among phylogeographic structure discarding incipient speciation, and contemporary spatial differentiation processes linked to drift-migration equilibrium models.</p>
Variant Call File (VCF) for Genome-wide polymorphism and genic selection in feral and domesticated lineages of Cannabis sativa
<p>A comprehensive understanding of the degree to which genomic variation is maintained by selection versus drift and gene flow is lacking in many important species such as <em>Cannabis</em> <em>sativa </em>(<em>C. sativa</em>), one of the oldest known crops to be cultivated by humans worldwide. We generated whole genome resequencing data across diverse samples of feralized (escaped domesticated lineages) and domesticated lineages of <em>C. sativa</em>. We performed analyses to examine population structure, and genome wide scans for FST, balancing selection, and positive selection. Our analyses identified evidence for sub-population structure and further support the Asian origin hypothesis of this species. Feral plants sourced from the U.S. exhibited broad regions on chromosomes 4 and 10 with high <span>𝐹̅</span>ST which may indicate chromosomal inversions maintained at high frequency in this sub-population. Both our balancing and positive selection analyses identified loci that may reflect differential selection for traits favored by natural selection and artificial selection in feral versus domesticated sub-populations. In the U.S. feral sub-population, we found six loci related to stress response under balancing selection and one gene involved in disease resistance under positive selection, suggesting local adaptation to new climates and biotic interactions. In the marijuana sub-population, we identified the gene <em>SMALLER TRICHOMES</em> <em>WITH VARIABLE BRANCHES 2 </em>to be under positive selection which suggests artificial selection for increased tetrahydrocannabinol yield. Overall the data generated, and results obtained from our study help to form a better understanding of the evolutionary history in <em>C. sativa</em>.</p>
SNiffles structural variant vcf SHRSP genome
<p>Variant cell format file generated by Sniffles2/SURVIVOR analysis</p>
Filtered VCF files for Bombus pascuorum and B. lapidarius
<p>Human-induced environmental impacts on wildlife are widespread, causing major biodiversity losses. One major threat is agricultural intensification, typically characterised by large areas of monoculture, mechanical tillage, and the use of agrochemicals; it leads to the fragmentation and loss of natural habitats, native vegetation, and nesting and breeding sites. Understanding the adaptability of insects to these changing environmental conditions is critical to predicting their survival. Bumblebees, key pollinators of wild and cultivated plants, are used as model species to assess insect adaptation to anthropogenic stressors. We investigated the effects of agricultural pressures on two common European bumblebees, <em>Bombus</em> <em>pascuorum</em> and <em>B</em>. <em>lapidarius</em>. Restriction-site Associated DNA Sequencing (RADSeq) was used to identify loci under selective pressure across agricultural-natural gradients over 97 locations in Europe. 191 unique loci in <em>B</em>. <em>pascuorum</em> and 260 in <em>B</em>. <em>lapidarius</em> were identified as under selective pressure, associated with agricultural stressors. Further investigation revealed candidate proteins for 26 loci in <em>B</em>. <em>pascuorum</em> including neurodevelopment proteins, a muscle protein, and a detoxification protein; and 53 loci in <em>B</em>. <em>lapidarius</em>, similarly including several neurodevelopmental, muscle, and detoxification proteins. These results provide insight into agriculture as a stressor for bumblebees and signal for conservation action in light of ongoing anthropogenic changes.</p>
EDX analysis on virgin (vCF) and recycled (rCF) carbon fibers
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VCF files for 100 high coverage baboon genomes from the Southwest National Primate Research Center
<p>Catalog of SNP and small indel variation in 100 high coverage (>20X) whole genome sequences from baboons (genus <em>Papio</em>) at the Southwest National Primate Research Center (SNPRC). These files use the Panu_2.0 baboon reference genome. See "Analysis of 100 high coverage genomes from a pedigreed captive baboon colony" by Robinson et al. 2019 for further details.</p>
Marmoset SNP Calls VCF
<p>Bgzipped vcf and tabix index files of marmoset SNP calls of 9 individuals on the calJac3 assembly.</p>
Comprehensive Structural Variant Benchmark Dataset: 1100 VCF files from long-read sequencing of 10 NCBI individuals
<p>We initially collected 10 NCBI individuals: HG002 family pedigree data (HG002 [son], HG003 [father], HG004 [mother]), the HG005 family pedigree data (HG005 [son], HG006 [father], HG007 [mother]), the NA12878 subject, the HG00096 subject, the HG00512 subject and the CHM13 subject. Then we used PacBio (CLR: Continuous Long Read, CCS: Circular Consensus Sequencing) and Nanopore (ONT) platforms, 5 aligners and 10 callers to construct the pipelines, with most parameters set to default values. After that, except for 6 invalid pipelines(pbmm2-Nanovar, lra-Picky, lra-delly, lra-NanoVar, lra-NanoSV, lra-pbsv), we obtain 1100 VCF files.</p>
The variation in VCF format called from Sporothrix datasets in Thailand using 2 DNA region
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Truvari Manuscript VCF files
<p>VCF Files with Truvari collapse of variants used as part of https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02840-6</p>
VCF files for D. serrata transposable elements
<p><span><span>Transposable elements are an important element of the complex genomic ecosystem. Transposable element insertion also appears to be bursty – either due to invasion of new transposable elements that are not yet repressed, de-repression due to instability of organismal defense systems, stress, or genetic variation in hosts. Here, we characterize the transposable element landscape in an important model <i>Drosophila</i>, <i>D. serrata</i>, and investigate variation in transposable element copy number between genotypes and in the population at large. We find that a subset of transposable elements are clearly related to elements annotated in <i>D. melanogaster</i> and <i>D. simulans</i>, suggesting they spread between species more recently than other transposable elements. We also find that some transposable elements proliferate in particular genotypes compared to population levels. In natural populations an active transposable element and a potentially permissive background would not be held in association as in inbred lines, thus this could be a product of inbreeding. Yet many of the inbred lines have actively proliferating transposable elements suggesting that active transposable elements are not uncommon and that genotypes vary in their permissiveness in populations. </span></span></p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.