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Detailed information for vg0330420931:

Variant ID: vg0330420931 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 30420931
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


CTCCACATCATTAAGAAACTAGTATTAGACACTACTCTCCCAATGCAAACACCACTATTCCATACTTAAATTAAATGCTACTTACCTCACATAATGTCTT[G/A]
GATGTTGTGTAGAAATCATGTCTCATGCAAGACTCTTTTATCATTTATTCACTTGCCACATCATTTTTCATTCTAGGTGACAGCTTATTTAATGCTATGG

Reverse complement sequence

CCATAGCATTAAATAAGCTGTCACCTAGAATGAAAAATGATGTGGCAAGTGAATAAATGATAAAAGAGTCTTGCATGAGACATGATTTCTACACAACATC[C/T]
AAGACATTATGTGAGGTAAGTAGCATTTAATTTAAGTATGGAATAGTGGTGTTTGCATTGGGAGAGTAGTGTCTAATACTAGTTTCTTAATGATGTGGAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.60% 5.60% 0.76% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 85.60% 12.10% 2.31% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 94.00% 2.90% 3.13% 0.00% NA
Tropical Japonica  504 89.50% 10.30% 0.20% 0.00% NA
Japonica Intermediate  241 50.60% 45.20% 4.15% 0.00% NA
VI/Aromatic  96 19.80% 79.20% 1.04% 0.00% NA
Intermediate  90 96.70% 3.30% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0330420931 G -> A LOC_Os03g53050.1 upstream_gene_variant ; 1260.0bp to feature; MODIFIER silent_mutation Average:56.766; most accessible tissue: Minghui63 flag leaf, score: 73.334 N N N N
vg0330420931 G -> A LOC_Os03g53030-LOC_Os03g53050 intergenic_region ; MODIFIER silent_mutation Average:56.766; most accessible tissue: Minghui63 flag leaf, score: 73.334 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0330420931 7.77E-06 NA mr1274 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0330420931 3.83E-06 1.19E-10 mr1281 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0330420931 3.29E-06 NA mr1842_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0330420931 6.77E-06 2.34E-09 mr1947_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251