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210 results for “single nucleotide polymorphisms”
Single Nucleotide Polymorphisms (SNPs) identified from the whole genome sequences of hilsa shad (Tenualosa ilisha) of the Bay of Bengal
<p>The data file contains 792,939 isolated SNPs identified by discoSnp++ v2.3.x (Uricaru et al., 2015) from the whole genome sequence of T. ilisha of the Bay of Bengal. The central sequence of length 2k-1 is seen in upper case, while the flanking sequences are seen in lower case. SNP_higher/lower: one of the two alleles. id: id of the SNP (each SNP has a unique id).</p> <p>FOR SNPs:</p> <p>P_i:pos_Alt1/Alt2: Information about a ith SNP (If more than a unique SNP is found, the following format is used: P_1:pos_Alt1/Alt2,P_2:pos_Alt1/Alt2,...</p> <p>pos: position of the SNP with respect to the starting position of the bubble, i.e. the starting of the upper case sequence.</p> <p>Alt1: One of the two alleles</p> <p>Alt2: the other</p> <p>FOR INDELs:</p> <p>P_1:pos_size_repeatSize</p> <p>pos: predicted position of the indel with respect to the starting position of the bubble, i.e. the starting of the upper case sequence.</p> <p>size: predicted size of the indel</p> <p>repeatSize: Size of the longest sequence both prefix of the indel and prefix of the sequence located just after the insertion.</p> <p>high/low: sequence complexity. If the sequence if of low complexity (e.g. ATATATATATATATAT) this variable would be low</p> <p>nb_pol: number of polymorphism.</p> <p>left_unitig_length: size of the full left extension.</p> <p>right_unitig_length: size of the right extension.</p> <p>left_contig_length: size of the full left extension.</p> <p>right_contig_length: size of the right extension.</p> <p>C1: number of reads mapping the central upper case sequence from the first read set.</p> <p>C2: number of reads mapping the central upper case sequence from the second read set.</p> <p>Q1 [if reads were given in fastq]: average phred quality of the central nucleotide from the mapped reads from the first read set.</p> <p>Q2 [if reads were given in fastq]: average phred quality of the central nucleotide from the mapped reads from the second read set.</p> <p>G1: Genotype of the variant in the first read set.</p> <p>G2: Genotype of the variant in the second read set.</p> <p>rank: ranks the predictions according to their read coverage in each condition favoring SNPs that are discriminant between conditions.</p>
Crown morphology in Norway spruce (Picea abies [Karst.] L.) as adaptation to mountainous environments is associated with single nucleotide polymorphisms (SNPs) in genes regulating seasonal growth rhythm
Trees growing at high altitude or latitude have to be adapted, amongst others, to the lower temperatures, a shorter vegetation period, heavier snow load and frost desiccation. Association between molecular genetic markers and climatic variables may provide evidence for the genetic control of climatic adaptation. With increasing genomic resources, several genes with importance to climatic adaptation are identified over a wide range of tree species. Commonly, circadian clock genes are linked to the adaptation to lower temperatures and especially to a shortened vegetation period, as they are regulating metabolic and phenological processes in the day-night shift and seasonal change. Potentially adaptive "candidate" genes associated with latitudinal and elevational gradients were identified in several Picea spp. Before molecular markers became available to study climatic adaptation, phenotypic traits measured in natural populations and/or common garden studies were used to search for their association with climate variables. In Norway spruce, the crown architecture is the most noticeable trait associated with altitude and the related environment. The mountainous narrow-crowned morphotype is characterised by superior resistance to snow breakage in regions with heavy snow fall. In total, the crown shape was assessed in 765 individual trees from mountainous regions in the Thuringian Forest, the Ore Mountains (Saxony) and Harz Mountains (Lower-Saxony/Saxony-Anhalt), and they were genotyped at 44 single nucleotide polymorphisms (SNPs) in 24 adaptive trait related candidate genes. Six SNPs in three genes, APETALA 2-like 3 (AP2L3), GIGANTEA (GI), and mitochondrial transcription termination factor (mTERF) were associated with variation in crown shape. GI has previously been identified in angiosperms and gymnosperms to be associated with temperature and growth cessation. Our results showed that crown morphology in Norway spruce is associated with genetic markers which are putatively involved in the complex process of genetic adaptation to climatic conditions at high altitudes.
RAD-seq generated single nucleotide polymorphisms resolve patterns of genetic diversity and structure of the freshwater mussel Ptychobranchus fasciolaris in glaciated and unglaciated regions of North America
<p>Included are the initial unfiltered SNP output from the STACKS pipeline, and the final filtered SNP dataset in VCF format used to do analysis in the manuscript titled "<span>RAD-seq generated single nucleotide polymorphisms resolve patterns of genetic diversity and structure of the freshwater mussel <em>Ptychobranchus fasciolaris </em>in glaciated and unglaciated regions of North America" which was submitted to <em>Hydrobiologia </em>in September 2024.</span></p>
Data from: Distances and their visualization in studies of spatial-temporal genetic variation using single nucleotide polymorphisms (SNPs)
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Data from: Evaluation of a single nucleotide polymorphism baseline for genetic stock identification of Chinook Salmon (Oncorhynchus tshawytscha) in the California Current Large Marine Ecosystem
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Data from: Discovery and characterization of single nucleotide polymorphisms in coho salmon, Oncorhynchus kisutch
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Single nucleotide polymorphism genotypes for the Australian blackspot shark and the milk shark in Northern Australian waters
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Data from: Discovery and characterization of single nucleotide polymorphisms in Chinook salmon, Oncorhynchus tshawytscha
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Data from: Comparing microsatellites and single nucleotide polymorphisms to evaluate genetic structure and diversity in wolverines (Gulo gulo) across Alaska and western Canada
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Single nucleotide polymorphisms, environmental data and R scripts used in the work: A donor registry: Genomic analyses of Posidonia australis seagrass meadows identifies adaptive genotypes for future-proofing
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Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru
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Single nucleotide polymorphisms related to vitamin D metabolism in patients with chronic obstructive pulmonary disease
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Single nucleotide Polymorphism (SNP) identification, genetic diversity, and population structure of Ryegrass from the northeastern highlands of Peru
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Single Nucleotide Polymorphisms (SNPs) data of Metarhizium species for Taxonomic Elucidation of M. anisopliae sensu lato
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Single nucleotide polymorphism (SNP) genotypes of Cashmere goat (Capra hircus) populations from Mongolia
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Genotyping-by-sequencing Single-nucleotide Polymorphism Dataset for Corynorhinus rafinesquii (CORA) and Myotis austroriparius (MYAU)
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Data from: Discovery and characterization of single nucleotide polymorphisms in two anadromous alosine fishes of conservation concern
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Genomic population structure of sympatric sexual and asexual populations in a parasitic wasp, Meteorus pulchricornis (Hymenoptera: Braconidae), inferred from six hundred single-nucleotide polymorphism loci
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Assessing gene flow between Dicranum scoparium Hedw. and D. bonjeanii De Not. (Dicranaceae) using single nucleotide polymorphisms (SNPs)
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Synthetic Datasets for Using synthetic datasets to bridge the gap between the promise and reality of basing health-related decisions on common single nucleotide polymorphisms
<p>Synthetic Dataset for Using synthetic datasets to bridge the gap between the promise and reality of basing health-related decisions on common single nucleotide polymorphisms, as published on F1000Research.</p>
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