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Detailed information for vg0336268568:

Variant ID: vg0336268568 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 36268568
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.95, A: 0.04, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTAAGCACGGCATGGCAGCTCATAAGGAACTTAATCCTAACAGCTTGGGTATAAAGTATGAACTGTCCATAGTGTACACTAGCCTTTGATATCAATCA[T/A]
AGAGTTTTTAACACCTAAATCTAGTAGCACACACTAATAAAGTGATACTCCCTGCATCCACTTTTGTGTTTGTTTAGATTTCGATCATAATCTAATAATG

Reverse complement sequence

CATTATTAGATTATGATCGAAATCTAAACAAACACAAAAGTGGATGCAGGGAGTATCACTTTATTAGTGTGTGCTACTAGATTTAGGTGTTAAAAACTCT[A/T]
TGATTGATATCAAAGGCTAGTGTACACTATGGACAGTTCATACTTTATACCCAAGCTGTTAGGATTAAGTTCCTTATGAGCTGCCATGCCGTGCTTAAAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.20% 41.60% 0.15% 0.00% NA
All Indica  2759 31.60% 68.20% 0.25% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 80.30% 19.70% 0.00% 0.00% NA
Indica I  595 11.30% 88.40% 0.34% 0.00% NA
Indica II  465 28.40% 71.40% 0.22% 0.00% NA
Indica III  913 42.20% 57.70% 0.11% 0.00% NA
Indica Intermediate  786 36.50% 63.10% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 71.10% 28.90% 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
vg0336268568 T -> A LOC_Os03g64200.1 downstream_gene_variant ; 4828.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0336268568 T -> A LOC_Os03g64200.2 downstream_gene_variant ; 4828.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0336268568 T -> A LOC_Os03g64190.1 intron_variant ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0336268568 T -> A LOC_Os03g64190.2 intron_variant ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0336268568 9.17E-06 2.40E-09 mr1587 Ind_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
vg0336268568 NA 7.49E-08 mr1212_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
vg0336268568 NA 4.02E-07 mr1233_2 Ind_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