DCARv2 Y2 Mapping Variants JBrowse VCF

Resource Type: 
File
File Type: 
VCF
Download: 
Download File NameAvailable atSizeMD5
y2map.dcar.vcf.gzCarrotOmics24.66MBef21d5aad6c7a89699afcb98b2b98f05
y2map.dcar.vcf.gz.tbiCarrotOmics143.2KBa5812d923a7d3aa044591a1d4275effc
Description: 

78,850 SNP variants from the F4 population 74,146. This is the VCF file used for JBrowse. See the linked analysis below for further details.

Note that this set of 78,850 SNPs was submitted to dbSNP at NCBI under BioProject PRJNA348698, however dbSNP dropped support for non-human genomes after publication, and the variants were not archived, and are not available there.

There is 1 relationship.
Relationships
The FASTA format, Carrot Genome Assembly DCARv2 Sequence Original Naming Scheme, is reference genome VCF, DCARv2 Y2 Mapping Variants JBrowse VCF.
References: 
The following records refer to this file:
Analysis
Organism
Analysis: 
NameDescription
Marker Development and and Linkage Map for Y₂, the Gene That Conditions β-Carotene Accumulation in Carrot

The F4 population 74,146 was derived from a cross between USDA carrot inbred line B493, an orange-rooted line, and QAL (Queen Anne’s Lace), a wild-type white-rooted carrot from the United States.

The TASSEL-GBS pipeline version 4.3.7 was used to call SNPs. The carrot genome assembly v2.0 was used as a reference to identify marker locations. SNPs were filtered for <10% missing data for genotype and marker, >10% minor allele frequency, and no more than two alleles.

The linkage map from this publication can be viewed at 2017 74,146

Data from this analysis can be viewed in JBrowse here.
Organism: 
NameCommon NameComment
Daucus carota subsp. sativus
Carrot
For a general overview of carrot, see the Carrot Facts Page
License: 
NameAttribution 4.0 International (CC BY 4.0)
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