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Detailed information for vg0113584309:

Variant ID: vg0113584309 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 13584309
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.53, A: 0.47, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


AAGCCCCCTTTGCCAGAGATCTGAAACAAAGCACAATTGCAGCCAGTTGTACATTGCTGACTCACACTCTGAAATCTGAACTTTGAAGTGTTACAAATAC[A/G]
TACATTTCTTCTGCCGCTGATCGAGCTCAATTGCCCGATCGAACTCTGCTACTGAGCCAGCTACATCTCCCTGTAATGCAAAGATAGGACGAACAGAAAA

Reverse complement sequence

TTTTCTGTTCGTCCTATCTTTGCATTACAGGGAGATGTAGCTGGCTCAGTAGCAGAGTTCGATCGGGCAATTGAGCTCGATCAGCGGCAGAAGAAATGTA[T/C]
GTATTTGTAACACTTCAAAGTTCAGATTTCAGAGTGTGAGTCAGCAATGTACAACTGGCTGCAATTGTGCTTTGTTTCAGATCTCTGGCAAAGGGGGCTT

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 54.50% 45.30% 0.21% 0.00% NA
All Indica  2759 72.30% 27.40% 0.29% 0.00% NA
All Japonica  1512 13.80% 86.20% 0.00% 0.00% NA
Aus  269 96.70% 2.60% 0.74% 0.00% NA
Indica I  595 50.40% 48.90% 0.67% 0.00% NA
Indica II  465 88.20% 11.40% 0.43% 0.00% NA
Indica III  913 76.70% 23.30% 0.00% 0.00% NA
Indica Intermediate  786 74.30% 25.40% 0.25% 0.00% NA
Temperate Japonica  767 1.30% 98.70% 0.00% 0.00% NA
Tropical Japonica  504 35.70% 64.30% 0.00% 0.00% NA
Japonica Intermediate  241 7.50% 92.50% 0.00% 0.00% NA
VI/Aromatic  96 71.90% 28.10% 0.00% 0.00% NA
Intermediate  90 47.80% 52.20% 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
vg0113584309 A -> G LOC_Os01g24090.2 missense_variant ; p.Met113Thr; MODERATE nonsynonymous_codon ; M113T Average:76.143; most accessible tissue: Zhenshan97 flower, score: 85.807 unknown unknown DELETERIOUS 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113584309 4.66E-06 1.19E-08 mr1064 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
vg0113584309 NA 4.12E-06 mr1073 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
vg0113584309 NA 4.54E-08 mr1193 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
vg0113584309 NA 2.37E-06 mr1291 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
vg0113584309 NA 1.89E-10 mr1471 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
vg0113584309 NA 2.23E-06 mr1534 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
vg0113584309 NA 8.65E-06 mr1677 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
vg0113584309 NA 1.63E-10 mr1722 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
vg0113584309 NA 9.40E-08 mr1815 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
vg0113584309 NA 2.03E-06 mr1830 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
vg0113584309 NA 1.08E-08 mr1519_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