Whole genome resequencing of Corylus heterophlla
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB31813 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Four groups of C57 mice were gavaged with CMC, ethanol, DEHP and ethanol+DEHP for 28 continuous days. At the end of the experiment, livers were harvested to carry out Whole genome resequencing, we found that metabolism related genes were significantly changed in the DEHP and ethanol+DEHP groups compared with control groups, but there was no significant change between them.
2019-01-01 | GSE121057 | GEO
Project description:Whole Genome sequences of Rabbits with varied phenotype
| PRJEB28783 | ENA
Project description:Whole genome resequencing of multiple Vitis sp. genotypes
| PRJEB44017 | ENA
Project description:Whole-genome resequencing of eight transcription factor mutants and one wild-type, in order to verify the T-DNA insertion site and its uniqueness.
2017-08-15 | GSE102126 | GEO
Project description:Whole genome resequencing of 125 chicken and two pooled populations including red jungle fowl and multiple populations of commercial broilers and layers
| PRJEB30270 | ENA
Project description:Atlantic puffin whole genome resequencing for population genomics analyses.
| PRJEB40631 | ENA
Project description:Macaca fascicularis Whole genome sequencing (Resequencing)
| PRJEB25088 | ENA
Project description:The next-generation sequencing technology coupled with the growing number of genome sequences opens the opportunity to redesign genotyping strategies for more effective genetic mapping and genome analysis. We have developed a high-throughput method for genotyping recombinant populations utilizing whole-genome resequencing data generated by the Illumina Genome Analyzer. A sliding window approach is designed to collectively examine genome-wide single nucleotide polymorphisms for genotype calling and recombination breakpoint determination. Using this method, we constructed a genetic map for 150 rice recombinant inbred lines with an expected genotype calling accuracy of 99.94% and a resolution of recombination breakpoints within an average of 40 kb. In comparison to the genetic map constructed with 287 PCR-based markers for the rice population, the sequencing-based method was approximately 20x faster in data collection and 35x more precise in recombination breakpoint determination. Using the sequencing-based genetic map, we located a quantitative trait locus of large effect on plant height in a 100-kb region containing the rice "green revolution" gene. Through computer simulation, we demonstrate that the method is robust for different types of mapping populations derived from organisms with variable quality of genome sequences and is feasible for organisms with large genome sizes and low polymorphisms. With continuous advances in sequencing technologies, this genome-based method may replace the conventional marker-based genotyping approach to provide a powerful tool for large-scale gene discovery and for addressing a wide range of biological questions.
| S-EPMC2694477 | biostudies-literature
Project description:Resequencing data for radish germplasm
| PRJEB44749 | ENA
Project description:Next-generation massively parallel sequencing technologies provide ultrahigh throughput at two orders of magnitude lower unit cost than capillary Sanger sequencing technology. One of the key applications of next-generation sequencing is studying genetic variation between individuals using whole-genome or target region resequencing. Here, we have developed a consensus-calling and SNP-detection method for sequencing-by-synthesis Illumina Genome Analyzer technology. We designed this method by carefully considering the data quality, alignment, and experimental errors common to this technology. All of this information was integrated into a single quality score for each base under Bayesian theory to measure the accuracy of consensus calling. We tested this methodology using a large-scale human resequencing data set of 36x coverage and assembled a high-quality nonrepetitive consensus sequence for 92.25% of the diploid autosomes and 88.07% of the haploid X chromosome. Comparison of the consensus sequence with Illumina human 1M BeadChip genotyped alleles from the same DNA sample showed that 98.6% of the 37,933 genotyped alleles on the X chromosome and 98% of 999,981 genotyped alleles on autosomes were covered at 99.97% and 99.84% consistency, respectively. At a low sequencing depth, we used prior probability of dbSNP alleles and were able to improve coverage of the dbSNP sites significantly as compared to that obtained using a nonimputation model. Our analyses demonstrate that our method has a very low false call rate at any sequencing depth and excellent genome coverage at a high sequencing depth.
| S-EPMC2694485 | biostudies-literature