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113 results for “VCF”
Genomic datasets of Laminaria digitata: Paired-end reads from dd-RADseq, reference genome assembly and filtered VCF
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Dsuite - fast D-statistics and related admixture evidence from VCF files
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Staphylococcus aureus VCF files: Risk Factors for Recurrent Staphylococcus aureus Bacteremia
<p>Background: To understand the clinical, bacterial, and host characteristics associated with recurrent Staphylococcus aureus bacteremia (R-SAB), patients with R-SAB were compared to contemporaneous patients with a single episode of SAB (S-SAB).<br> Methods: All SAB isolates underwent spa genotyping. All isolates from R-SAB patients underwent Pulsed-Field Gel Electrophoresis (PFGE). PFGE-indistinguishable pairs from 40 patients underwent whole genome sequencing (WGS). Acute phase plasma from R-SAB and S-SAB patients was matched 1:1 for age, race, gender, and bacterial genotype and underwent cytokine quantification using 25-analyte multiplex bead array. Results: R-SAB occurred in 69 (9.1%) of the 756 study patients. Of the 69 patients, 30 experienced relapse (43.5%) and 39 reinfection (56.5%). Age, race, hemodialysis dependence, presence of foreign body, MRSA, and persistent bacteremia were individually associated with likelihood of recurrence. Multivariate risk modeling revealed that African American (AA) hemodialysis patients were nearly two times more likely (OR = 9.652 [5.402 – 17.418]) than White hemodialysis patients (OR = 4.53 [1.696 – 10.879]) to experience R-SAB. WGS confirmed PFGE interpretations in all cases. Median RANTES levels in acute phase plasma from the initial episode of SAB were higher in R-SAB than in matched S-SAB controls ( P = 0.0053, False Discovery Rate < 0.10). <br> Conclusion: This study identified several risk factors for R-SAB. The largest risk for R-SAB is among AA hemodialysis patients. Higher RANTES levels in R-SAB compared to<br> matched controls warrants further study.</p>
Adaptation by copy number variation increases insecticide resistance in the fall armyworm (vcf files)
<p>Here, I deposite vcf files used for a paper, entitled 'Adaptation by copy number variation increases insecticide resistance in the fall armyworm'.</p> <p>genotype.vcf and SNP.filtered.vcf.gz have the information of CNVs and SNPs, respectively. </p>
VCF file for a population of Drosophila melanogaster
<p>This file is the set of single nucleotide polymorphisms and insertion/deletions in a population of Drosophila melanoagaster. The zipped file is in a simple text file. This VCF file is part of the following larger body of work: <strong>Patterns of genetic regulation of expression variation in a natural population of Drosophila melanogaster provide evidence for buffering and GRN robustness</strong></p>
QTL script and VCF files - GENETIC ARCHITECTURE OF FLOWERING-TIME VARIATION IN BRACHYPODIUM DISTACHYON
<p>Supplemental data for the article:</p> <p>GENETIC ARCHITECTURE OF FLOWERING-TIME VARIATION IN BRACHYPODIUM DISTACHYON (Woods et al., 2016).</p> <p>Supplemental data includes:</p> <ul> <li> <p>A folder named “Data”, which contains:</p> <ol> <li> <p><strong>Raw genotypic data</strong>. Data showing the parental genotype in a RIL population (F7; Bd21 X Bd1-1)</p> </li> <li> <p><strong>Raw phenotypic data</strong>. Flowering time (leaves and days to flowering) of the RIL population in different growth environments.</p> </li> <li> <p><strong>The genetic map </strong>(see material and methods section of Woods et al., 2016 for additional information).</p> </li> <li> <p><strong>Gene positions.</strong> A file containing the position of annotated genes on the Brachypodium distachyon genome V2.1. Data from Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html).</p> </li> </ol> </li> <li> <p>The<strong> R script</strong> used for the QTL analysis (Final_script.R).</p> </li> <li> <p><strong>VCF files of the loci of interest</strong>. A folder called “VCF” includes the VCF files of the genes presented in Fig. 6 (VRN1, PHYC, VRN2, and FD). </p> </li> </ul> <p> </p>
Drosophila simulans VCF: The set of single nucleotide polymorphisms and insertion/deletions in a population of 170 Drosophila simulans lines.
<p>Heritable phenotypic variation in natural populations exceeds the levels predicted under mutation-selection balance where purifying selection removes variation. Balancing selection, inefficient or weak selection, polygenic adaptation, and non-equilibrium populations are all possible explanations for excess variation. Yet, available genomic data indicate an abundance of directional selection. One potential explanation is that fleeting directional selection drives beneficial mutations to high frequency in rapid waves resulting in many intermediate frequency haplotypes. This hypothesis is supported by the genomic data from a panel of 170 D. simulans genotypes established from a single stable population which show evidence for an abundance of incomplete soft sweeps. Demography, admixture, and balancing selection cannot entirely explain the patterns in these data, while transient selective sweeps can account for all the patterns of variation observed in this population. One interpretation is that constant environmental shifts rapidly change the optimal phenotype within Drosophila populations, leaving a signature of adaptive responses.</p>
VCF files and regression analyses for: Assessing fine-scale pondscape connectivity with amphibian eyes: an integrative approach using genomic and capture-mark-recapture data
<p><span>In the face of habitat loss, preserving functional connectivity is essential to maintain genetic diversity and the demographic dynamics required for the viability of biotic communities. This requires knowledge of the dispersal behavior of target species, which can be modeled as kernels, or probability density functions of dispersal distances at increasing geographic distances. We present an integrative approach to investigate the relationships between genetic connectivity and demographic parameters in organisms with low vagility focusing on five syntopic pond-breeding amphibians. We genotyped 1,056 individuals of two anuran and three urodele species (1,732–3,913 SNPs per species) from populations located in a landscape comprising 64 ponds to characterize fine-scale genetic structure in a comparative framework and combined this genetic data with information obtained in a previous two-year capture-mark-recapture (CMR) study. Specifically, we contrasted graphs reconstructed from genomic data with connectivity graphs based on dispersal kernels and demographic information obtained from CMR data from previous studies and assessed the effects of population size, population density, geographical distances, inverse movement probabilities and the presence of habitat patches potentially functioning as stepping stones on genetic differentiation. Our results suggest a significant influence of local population sizes on patterns of genetic connectivity at small spatial scales. In addition, m</span><span>ovement records and cluster-derived kernels provide robust inferences on most likely dispersal paths that are consistent with </span><span>genomic inferences on genetic connectivity. The integration of genetic and CMR data holds great potential for understanding genetic connectivity at spatial scales relevant to individual organisms, with applications for the implementation of management actions at the landscape level. </span></p>
Mergus octosetaceus ddRAD data (vcf file)
<p>This VCF file contains SNPs derived from 46 individuals of the <i>Mergus octosetaceus </i>species. The data was obtained using the Double digest restriction-site associated sequencing (ddRAD-seq) methodology and processed through the Stacks <i>de novo</i> pipeline.</p>
Mergus octosetaceus GBS data (vcf file)
<p>This VCF file contains SNPs derived from 30 individuals of the <i>Mergus octosetaceus </i>species. The data was obtained using the Genotyping by Sequencing (GBS) methodology and processed through the Stacks <i>de novo</i> pipeline.</p>
Rescued Phased VCF for GIAB HG001
<p><strong>The GIAB VCF file contained anomalies that elicited run-time errors from both LRphase and WhatsHap. This VCF is noncompliant with the VCF 4.3 specification (https://samtools.github.io/hts-specs/VCFv4.3.pdf) in at least two ways: 1) Phase Set (PS) tags within genotype fields contain strings instead of 32-bit integers. 2) Sample columns in the VCF column header are labeled ”INTEGRATION” rather than containing the sample name. We also found ~25,000 records with malformed genotype records, which contained extra fields not defined in the format string. Finally, we encountered errors from WhatsHap that suggested at least a subset of indel records are also malformed. Neither program would run successfully without correcting these errors, but we were able to rescue the VCF using a custom Python script. Briefly, we transliterated PS tag strings to integer values by concatenating a unique integer with the chromosome number for each record (24, 25, and 26, for chromosomes X, Y, and M, respectively). This ensured that all phase sets have integer labels and only included variants on the same chromosome. We defined an additional format tag, OPS, under which we stored the original PS tag values. Likewise, the “INTEGRATION” label in the column name header was replaced with the sample name, “HG001”. Variants with malformed genotype fields were rescued by removing the fields not defined in the format string. Since we were unable to identify the direct cause for WhatsHap errors related to indel record parsing, we filtered out all records for indels and structural variants, leaving only SNV records in the VCF.</strong></p>
VCF file created by Synteny and Rearrangement Indicator software
<p>VCF file created by Synteny and Rearrangement Indicator software for the rat reference genome mRatBN7.2 and the SHRSP genome assembly</p>
VCF datasets and analysis scripts for: The combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability
<p>Global warming is increasingly exacerbating biodiversity loss. Populations locally adapted to spatially heterogeneous environments may respond differentially to climate change, but this intraspecific variation has only recently been considered when modelling vulnerability under climate change. Here, we incorporate intraspecific variation in genomic offset and ecological niche modelling to estimate climate change-driven vulnerability in two bird species in the Sino-Himalayan Mountains. We found that the cold-tolerant populations show higher genomic offset but risk less challenge for niche suitability decline under future climate than the warm-tolerant populations. Based on a genome-niche index estimated by combining genomic offset and niche suitability change, we identified the populations with the least genome-niche interruption as potential donors for evolutionary rescue, i.e., the populations tolerant to climate change. We evaluated potential rescue routes via a landscape genetic analysis. Overall, we demonstrate that the integration of genomic offset, niche suitability modelling, and landscape connectivity can improve climate change-driven vulnerability assessments and facilitate effective conservation management.</p>
VCF and phenotypes of 314 sweetpotato
<p>This dataset is consists of two parts, one is derived from the SNP calling from 314 sweetpotato germplasm resources, and the reference genome was a set of subgenomes of "Xushu18"; and another is the phenotypes of these germplasm resources. The related article is "Resequencing of sweetpotato germplasm resources reveals key loci associated with multiple agronomic traits".</p>
VCF for neutral data set and potential connectivity matrices of Harpagifer antarcticus, along the Western Antarctic Peninsula
<p>Connectivity is a fundamental process of population dynamics in marine ecosystems. In the last decade, with the emergence of new methods, combining different approaches to understand the patterns of connectivity among populations and their regulation has become increasingly feasible. The Western Antarctic Peninsula (WAP) is characterized by complex oceanographic dynamics, where local conditions could act as barriers to population connectivity. Here, the notothenioid fish <em>Harpagifer antarcticus</em>, a demersal species with a complex life cycle (adults with poor swim capabilities and pelagic larvae), was used to assess connectivity along the WAP by combining biophysical modeling and population genomics methods. Both approaches showed congruent patterns. Areas of larvae retention and low potential connectivity, observed in the biophysical model output, coincide with four genetic groups within the WAP: (1) South Shetland Islands, (2) Bransfield Strait, (3) the central, and (4) the southern area of WAP (Marguerite Bay). These genetic groups exhibited limited gene flow between them, consistent with local oceanographic conditions, which would represent barriers to larval dispersal. The joint effect of geographic distance and larval dispersal by ocean currents, had a greater influence on the observed population structure, than each variable evaluated separately. The combined effect of geographic distance and a complex oceanographic dynamic would be generating limited levels of population connectivity in the fish <em>H. antarcticus</em>along the WAP. Based on this population connectivity estimations, priority areas for conservation were discussed, considering the Marine Protected Area proposed for this threatened region of the Southern Ocean.</p>
A high coverage Mesolithic aurochs genome and effective leveraging of ancient cattle genomes using whole genome imputation. -- VCF file
<p>This is the open-access VCF file that was created in the article: "<strong>A high coverage Mesolithic aurochs genome and effective leveraging of ancient cattle genomes using whole genome imputation."</strong></p> <p><strong>Information about the filtering steps can be found in the method section.</strong></p> <p>Extra information on the sample IDs can be found in the Supplementary tables.</p>
De novo assembly of SNPs in VCF format for 112 individualss of Campylorhynchus in western Ecuador
<p>Climate variability has a significant impact on the evolution of biodiversity, which results in genetic and phenotypic diversity within species. A balance between gene flow and selection maintains changes in the frequency of genetic and phenotypic variants that occur along an environmental gradient. Here, we investigate a hybrid zone in western Ecuador involving C. zonatus, C. fasciatus, and admixed populations. We hypothesized that different ecological preferences and geographical distances result in limited dispersal between populations along the precipitation gradient in western Ecuador.</p> <p>In the context of testing IBE and IBD shaping distributions of C. zonatus, C. fasciatus, and potential hybrids, we asked (1) Is there evidence of genetic admixture and introgression between these taxa in Western Ecuador? And (2) What is the relative contribution of IBE and IBD on patterns of genetic differentiation and admixture patterns? We analyzed 4409 SNPs from the blood of 112 individuals sequenced using ddRadSeq. The most likely clusters ranged from K=2-4, corresponding to categories defined by geographic origins, known phylogenetics, and physical or ecological constraints. Evidence for IBE was weak but stronger for IBD. We observed gradual changes in genetic admixture between C. f. pallescens and C. zonatus along the environmental gradient. Genetic differentiation of the two populations of C. f. pallescens could be driven by a previously undescribed potential physical barrier near the center of western Ecuador. Lowland habitats in this region may be limited due to the proximity of the Andes to the coastline, limiting dispersal and gene flow, particularly among dry-habitat specialists.</p>
VCF File containg replicate RAD-seq genotype calls for four Populs alba x Populus tremula hybrids.
<p>VCF file used to estimate RAD-seq genotyping errors in Bresadola et al. (2019).</p>
Crab Eating Macaque SNP Calls VCF
<p>Bgzipped vcf and tabix index files of crab eating macaque SNP calls of 26 individuals on the macFas5 assembly.</p>
Rhesus Macaque SNP Calls VCF
<p>Bgzipped vcf and tabix index files of rhesus macaque SNP calls of 526 individuals on the rheMac8 assembly.</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)
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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.