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Detailed information for vg0422162033:

Variant ID: vg0422162033 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 22162033
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


TATTATTATTAAAATATAATACAATACTAAATTTAATGAAACTAATTTGGTGTTTAAAATGTTGCTAATTTTTTCTATAAACTTAGTTAAACTTAATAAA[G/A]
TTTAACTTAAAAAAAGTCAAAGTTAATTGTGTCAATTATGTATACTGACATGGGAGACGATGGCGTAGAGGGGGAGCGTGCTGTAGCTGCAGAGGACCTG

Reverse complement sequence

CAGGTCCTCTGCAGCTACAGCACGCTCCCCCTCTACGCCATCGTCTCCCATGTCAGTATACATAATTGACACAATTAACTTTGACTTTTTTTAAGTTAAA[C/T]
TTTATTAAGTTTAACTAAGTTTATAGAAAAAATTAGCAACATTTTAAACACCAAATTAGTTTCATTAAATTTAGTATTGTATTATATTTTAATAATAATA

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 67.70% 31.80% 0.51% 0.00% NA
All Indica  2759 45.40% 53.70% 0.87% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 37.10% 61.50% 1.34% 0.00% NA
Indica II  465 23.90% 75.70% 0.43% 0.00% NA
Indica III  913 56.60% 42.80% 0.55% 0.00% NA
Indica Intermediate  786 51.40% 47.50% 1.15% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0422162033 G -> A LOC_Os04g36670.1 downstream_gene_variant ; 2787.0bp to feature; MODIFIER silent_mutation Average:44.957; most accessible tissue: Callus, score: 82.55 N N N N
vg0422162033 G -> A LOC_Os04g36680.1 intron_variant ; MODIFIER silent_mutation Average:44.957; most accessible tissue: Callus, score: 82.55 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0422162033 NA 1.14E-06 mr1063 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
vg0422162033 NA 6.44E-10 mr1352 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
vg0422162033 NA 3.33E-06 mr1184_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
vg0422162033 NA 1.46E-06 mr1278_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
vg0422162033 6.53E-06 NA mr1738_2 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
vg0422162033 5.13E-08 5.13E-08 mr1738_2 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