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Detailed information for vg0234310220:

Variant ID: vg0234310220 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 34310220
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.03, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


ACACAGTGCAATTGTGCAAACTTCGTGTGTAGTGCAAACCTGAAAACTACCACATGATATATAAATGGACGTCTAAGATTTGTTCACGCCATCCATTTGC[G/A]
TATCCTACGATAGTTTTTAGATTTACACTACATATGAAGTTTGCACTATTTATTGATGTCATATTGCCATGCACAGATATCCGATGATACAATCTAAGAA

Reverse complement sequence

TTCTTAGATTGTATCATCGGATATCTGTGCATGGCAATATGACATCAATAAATAGTGCAAACTTCATATGTAGTGTAAATCTAAAAACTATCGTAGGATA[C/T]
GCAAATGGATGGCGTGAACAAATCTTAGACGTCCATTTATATATCATGTGGTAGTTTTCAGGTTTGCACTACACACGAAGTTTGCACAATTGCACTGTGT

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 62.00% 37.90% 0.19% 0.00% NA
All Indica  2759 43.90% 55.90% 0.29% 0.00% NA
All Japonica  1512 97.00% 3.00% 0.00% 0.00% NA
Aus  269 59.50% 40.50% 0.00% 0.00% NA
Indica I  595 48.20% 51.30% 0.50% 0.00% NA
Indica II  465 44.90% 55.10% 0.00% 0.00% NA
Indica III  913 39.10% 60.70% 0.22% 0.00% NA
Indica Intermediate  786 45.40% 54.20% 0.38% 0.00% NA
Temperate Japonica  767 97.70% 2.30% 0.00% 0.00% NA
Tropical Japonica  504 97.40% 2.60% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 6.20% 0.00% 0.00% NA
VI/Aromatic  96 34.40% 65.60% 0.00% 0.00% NA
Intermediate  90 65.60% 33.30% 1.11% 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
vg0234310220 G -> A LOC_Os02g56040.1 upstream_gene_variant ; 2491.0bp to feature; MODIFIER silent_mutation Average:64.412; most accessible tissue: Callus, score: 77.368 N N N N
vg0234310220 G -> A LOC_Os02g56060.1 upstream_gene_variant ; 2486.0bp to feature; MODIFIER silent_mutation Average:64.412; most accessible tissue: Callus, score: 77.368 N N N N
vg0234310220 G -> A LOC_Os02g56050.1 intron_variant ; MODIFIER silent_mutation Average:64.412; most accessible tissue: Callus, score: 77.368 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0234310220 NA 1.05E-06 mr1020_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
vg0234310220 NA 1.79E-10 mr1478_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
vg0234310220 NA 6.92E-09 mr1659_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
vg0234310220 NA 8.02E-06 mr1971_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