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Sequence variants

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Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: II: Carcass merit traits

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The value of the imputed 7.8 M whole genome sequence variants on GWAS. genotyped with the Affymetrix HD panel, and a panel of 1570 animals with WGS variants from run 5 of the 1000 Bull Genomes Project, we achieved an average imput- ation accuracy of 96.41% on whole genotype sequence variants using FImpute 2.2 [28].

GSAlign: An efficient sequence alignment tool for intra-species genomes

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GSAlign: an efficient sequence alignment tool for intra-species genomes. Both fields require sequence alignment to discover sequence conservation and variation. A wrong sequence alignment would produce false sequence variants.. Results: In this study, we present GSAlign that handles large genome sequence alignment efficiently and identifies sequence variants from the alignment result. GSAlign is an efficient sequence alignment tool for intra-species genomes.

Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: I: Feed efficiency and component traits

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The amount of additive gen- etic variance explained per sequence variant was calcu- lated for each functional class by the additive genetic variance captured by the DNA variants in the functional class divided by the number of DNA variants in the class..

Natural and pathogenic protein sequence variation affecting prion-like domains within and across human proteomes

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For estima- tion of the range of theoretical aggregation propensity scores based on observed sequence variants, reference sequences including >.

Autosomal recessive loci contribute significantly to quantitative variation of male fertility in a dairy cattle population

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We detected 48,121 sequence variants within ±3 Mb of the top haplotype, of which 778 were compatible with the recessive inheritance of the top. Of the compatible variants, six reside in protein-coding sequences: four synonymous variants in ZP2 (rs110876106, BTA C >. The frequency of the top haplotype in the BSW population is 0.26. 4 Detailed view of a QTL for bull fertility on BTA25.

Investigating the impact of reference assembly choice on genomic analyses in a cattle breed

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The imputed data with variants aligned to the ARS- UCD1.2 and UOA_Angus_1 assembly respectively, con- tained genotypes at and sequence variants.. Number of variants detected per kilo base pair (Kb) along autosomal sequences of 161 BSW samples when aligned to the ARS-UCD1.2 (blue) and UOA_Angus_1 (orange) assembly.. Assembly ARS-UCD1.2 is displayed in the top panel (blue) and assembly UOA_Angus_1 is displayed as a mirror image in the bottom panel (orange)..

Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

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Of the 48,224 SNP that were either polymorphic or fixed for the alternate allele in the array-called geno- types and were also present in the raw and filtered sequence variants, re- spectively. 1232 SNP of the Illumina PorcineSNP60 BeadChip complement were missing in the sequenced set because they were either genotyped as INDEL or multiallelic sites using GATK and thus excluded from the comparison due to incompatible alleles. 983 and 1041 SNP were not among the raw and filtered sequence variants,

Genetic mapping of novel modifiers for ApcMin induced intestinal polyps’ development using the genetic architecture power of the collaborative cross mice

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Except for a small number of de-novo mutations arising during breeding, all sequence variants segregating in the CC lines should also segregate in the CC founders. Briefly, except for a small number of de-novo mutations arising during breeding, all sequence variants segregating in the CC should also segregate in the CC founders.

Exploring protocol bias in airway microbiome studies: One versus two PCR steps and 16S rRNA gene region V3 V4 versus V4

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Comparison of the number of sequences and amplicon sequence variants (ASVs) retained at each bioinformatic filtering step for procedural samples (PSB, PBAL, OW, NCS) collected from 14 participants (n = 56).. The table presents an overview of the sequence count per ASV obtained after V3 V4 sequencing of mock community sample HM-783D following setup 1.. The table presents an overview of the sequence count per ASV obtained after V4 sequencing of mock community sample HM-783D following setup 2..

Transcriptomic and presence/absence variation in the barley genome assessed from multi-tissue mRNA sequencing and their power to predict phenotypic traits

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The number of variants gives the mean number of features available for predictions in each scenario or for the combined predictors the weight of sequence variants (SV s )/expression presence/absence variation (ePAV s )/gene expression (T s ) resulting in the highest prediction accuracy.

Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units

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The raw demultiplexed sequence data are available in the NCBI Sequence Read Archive under accession numbers PRJNA602824 (field soil dataset), PRJNA524079 (plant-related experiment) and PRJNA601852 (bacterial and fungal mock) and PRJNA601863 (simulated bacterial and fungal mock).. Emergence shapes the structure of the seed microbiota. Pathogen-induced activation of disease- suppressive functions in the endophytic root microbiome.

Cruxome: A powerful tool for annotating, interpreting and reporting genetic variants

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Getting sequence ” tools: displays flanking sequence of a given site in the reference genome.. The position, reference sequence and the type of variants are shown in the above three rows. Locus search ” tool: calculates the frequency of variants in a given region in all samples in the personal knowledge base. The online version contains supplementary material available at https://doi.. org/10.1186/s .

Analysis of functional variants in mitochondrial DNA of Finnish athletes

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The number of such var- iants was counted in each sequence and the count of rare functional variants included those with minor allele fre- quency (MAF) less than 1% in MITOMAP (http://www.. mitomap.org) and common functional variants included those with MAF ≥ 1%. A) that connect L3 and rCRS in the phylogeny..

Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants

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For samples with a high number of mismatches, either nanopore or Illumina sequence did not have an adequate coverage in some segments of the genome (adequate coverage was defined as >. Nanopore sequencing can be successfully and cost- effectively employed for full genome sequencing of HCV. Nano-Q was also able to identify within-host variants without an autologous reference sequence..

Towards a better understanding of the low recall of insertion variants with short-read based variant callers

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A better control could prob- ably be achieved with sequence-resolved variants and by taking into account the observed characteristics of the dif- ferent insertion types. In this work, we produced a detailed characterization of the insertion variants in a given human individual..

Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene

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Cloning of novel human P4HB splice variants. The sequence of P4HB -021 as used as template for isoform validation.. P4HB gene and splice variant information.. Table with information about GTEx RNA- seq data is presented as dataset.. Quantification of P4HB splice variants to detect the fraction of isoform abundance normalized by P4HB gene.

Genome sequence of the model rice variety KitaakeX

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N50 = minimum sequence length needed to cover 50% of the genome. A range of variants was detected by com- paring the BAC clones to the assembly. The overall error rate in the BAC clones is 0.09%, indicat- ing the high quality of this assembly (for detailed information, see Additional file 1).. We predicted 35,594 protein-coding genes in the Kitaa- keX genome (Table 1.c, Additional file 2: Table S12), representing 31.5% genic space of the assembled genome size (Table 1).

Assessment of branch point prediction tools to predict physiological branch points and their alteration by variants

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For the tools SVM-BPfinder, BPP and Branchpointer, we narrowed the browsed sequence by these 3 tools to include 1 to 200 nt upstream of the 3’ss.. LaBranchoR and RNABPS need a 70 nt long sequence, and the browsed sequence was the 70 last nt of the in- tron. The use of the different tools did not need param- eter settings, except for SVM-BPfinder.

Genome-wide association analysis identified both RNA-seq and DNA variants associated to paratuberculosis in Canadian Holstein cattle ‘in vitro’ experimentally infected macrophages

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Evaluation of the accuracy of imputed sequence variant genotypes and their utility for causal variant detection in cattle

Concordance rate between copy number variants detected using either high- or medium-density single nucleotide polymorphism genotype panels and the potential of imputing copy number variants from flanking high density single nucleotide polymorphism haplotypes in cattle

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Concordance rate between copy number variants detected using either high- or medium-density single nucleotide. polymorphism genotype panels and the potential of imputing copy number variants from flanking high density single nucleotide polymorphism haplotypes in cattle. The main aim here was to determine if it is possible to impute copy number variants (CNVs) using the flanking single nucleotide polymorphism (SNP) haplotype structure in cattle.