Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0431905664:

Variant ID: vg0431905664 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31905664
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


AGTTCAAAGTTTTGTGGAAAAGATAGAAGAAAAAATTGTATGCATGAACAAAAACAACCCATATTGATAACTTTCTCATTTCTGCAAGGAAAAATCTGGT[G/A]
TGTTCATACTTCATAAAAACACAGAAAAAAATTTGGGGATAAAATGGAAGATTGCTTTAAATCAGGAAGGGATGAGGAGACAAGCTAAGTGAAGAAACTT

Reverse complement sequence

AAGTTTCTTCACTTAGCTTGTCTCCTCATCCCTTCCTGATTTAAAGCAATCTTCCATTTTATCCCCAAATTTTTTTCTGTGTTTTTATGAAGTATGAACA[C/T]
ACCAGATTTTTCCTTGCAGAAATGAGAAAGTTATCAATATGGGTTGTTTTTGTTCATGCATACAATTTTTTCTTCTATCTTTTCCACAAAACTTTGAACT

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 94.70% 5.30% 0.02% 0.00% NA
All Indica  2759 93.10% 6.90% 0.04% 0.00% NA
All Japonica  1512 97.10% 2.90% 0.00% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 94.30% 5.50% 0.17% 0.00% NA
Indica II  465 92.00% 8.00% 0.00% 0.00% NA
Indica III  913 91.00% 9.00% 0.00% 0.00% NA
Indica Intermediate  786 95.20% 4.80% 0.00% 0.00% NA
Temperate Japonica  767 94.80% 5.20% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0431905664 G -> A LOC_Os04g53530.1 downstream_gene_variant ; 4972.0bp to feature; MODIFIER silent_mutation Average:50.473; most accessible tissue: Zhenshan97 flower, score: 83.499 N N N N
vg0431905664 G -> A LOC_Os04g53544.1 downstream_gene_variant ; 4586.0bp to feature; MODIFIER silent_mutation Average:50.473; most accessible tissue: Zhenshan97 flower, score: 83.499 N N N N
vg0431905664 G -> A LOC_Os04g53540.1 intron_variant ; MODIFIER silent_mutation Average:50.473; most accessible tissue: Zhenshan97 flower, score: 83.499 N N N N
vg0431905664 G -> A LOC_Os04g53540.4 intron_variant ; MODIFIER silent_mutation Average:50.473; most accessible tissue: Zhenshan97 flower, score: 83.499 N N N N
vg0431905664 G -> A LOC_Os04g53540.2 intron_variant ; MODIFIER silent_mutation Average:50.473; most accessible tissue: Zhenshan97 flower, score: 83.499 N N N N
vg0431905664 G -> A LOC_Os04g53540.3 intron_variant ; MODIFIER silent_mutation Average:50.473; most accessible tissue: Zhenshan97 flower, score: 83.499 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431905664 NA 9.64E-06 mr1310 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
vg0431905664 NA 1.84E-08 mr1570 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
vg0431905664 3.29E-06 3.29E-06 mr1855 Jap_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