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Detailed information for vg0420952139:

Variant ID: vg0420952139 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 20952139
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.55, A: 0.44, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


CATTCCTCATACCTAAAATTAACTATTTAAAATTCCACAAAGTGTAATATATGGAAATTTATAAAACTCTCCTATGCTCAAATTTCACCCGAATTAATAA[G/A]
CAATAAAATCTGCTAATAAAAATGTGCACTCCTACCAGCAAATCTCTGCTAGATCACACCATAAAATCCTTCCACAATCAAAGAGCTTAAATCTTCCCCC

Reverse complement sequence

GGGGGAAGATTTAAGCTCTTTGATTGTGGAAGGATTTTATGGTGTGATCTAGCAGAGATTTGCTGGTAGGAGTGCACATTTTTATTAGCAGATTTTATTG[C/T]
TTATTAATTCGGGTGAAATTTGAGCATAGGAGAGTTTTATAAATTTCCATATATTACACTTTGTGGAATTTTAAATAGTTAATTTTAGGTATGAGGAATG

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 53.80% 46.10% 0.13% 0.00% NA
All Indica  2759 36.00% 63.80% 0.18% 0.00% NA
All Japonica  1512 91.00% 8.90% 0.07% 0.00% NA
Aus  269 23.40% 76.60% 0.00% 0.00% NA
Indica I  595 76.60% 23.40% 0.00% 0.00% NA
Indica II  465 12.90% 86.90% 0.22% 0.00% NA
Indica III  913 29.40% 70.30% 0.33% 0.00% NA
Indica Intermediate  786 26.70% 73.20% 0.13% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 78.00% 22.00% 0.00% 0.00% NA
Japonica Intermediate  241 90.90% 8.70% 0.41% 0.00% NA
VI/Aromatic  96 54.20% 45.80% 0.00% 0.00% NA
Intermediate  90 63.30% 36.70% 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
vg0420952139 G -> A LOC_Os04g34610.1 upstream_gene_variant ; 3810.0bp to feature; MODIFIER silent_mutation Average:60.81; most accessible tissue: Zhenshan97 flower, score: 78.317 N N N N
vg0420952139 G -> A LOC_Os04g34630.1 upstream_gene_variant ; 2337.0bp to feature; MODIFIER silent_mutation Average:60.81; most accessible tissue: Zhenshan97 flower, score: 78.317 N N N N
vg0420952139 G -> A LOC_Os04g34620.1 intron_variant ; MODIFIER silent_mutation Average:60.81; most accessible tissue: Zhenshan97 flower, score: 78.317 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0420952139 5.74E-06 NA mr1217 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
vg0420952139 NA 3.08E-06 mr1404 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
vg0420952139 NA 1.68E-07 mr1659 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
vg0420952139 8.84E-07 NA mr1845 Jap_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