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Detailed information for vg0200456649:

Variant ID: vg0200456649 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 456649
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, G: 0.02, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


CGCATTCTTTTTATCAGCATGCATAAGAATTAAGGAGTCATCAGCAAATGAAAGATGGGAAACCATTGGGGCATCTCTGCATACTCTAATCCCTTCCAAT[G/C]
CTCCATTCTCCTCCACTTGTTGGATCATACTTGATAGGCCTTCTGCAACAAAGAGAAATAGGTAAGGGGATAGGGGATCCCCTTGCCTGATTCCTCTTGT

Reverse complement sequence

ACAAGAGGAATCAGGCAAGGGGATCCCCTATCCCCTTACCTATTTCTCTTTGTTGCAGAAGGCCTATCAAGTATGATCCAACAAGTGGAGGAGAATGGAG[C/G]
ATTGGAAGGGATTAGAGTATGCAGAGATGCCCCAATGGTTTCCCATCTTTCATTTGCTGATGACTCCTTAATTCTTATGCATGCTGATAAAAAGAATGCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.10% 46.90% 0.04% 0.00% NA
All Indica  2759 79.70% 20.30% 0.07% 0.00% NA
All Japonica  1512 1.90% 98.10% 0.00% 0.00% NA
Aus  269 61.00% 39.00% 0.00% 0.00% NA
Indica I  595 61.50% 38.30% 0.17% 0.00% NA
Indica II  465 77.80% 22.20% 0.00% 0.00% NA
Indica III  913 88.60% 11.30% 0.11% 0.00% NA
Indica Intermediate  786 84.10% 15.90% 0.00% 0.00% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 3.20% 96.80% 0.00% 0.00% NA
Japonica Intermediate  241 3.70% 96.30% 0.00% 0.00% NA
VI/Aromatic  96 78.10% 21.90% 0.00% 0.00% NA
Intermediate  90 46.70% 53.30% 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
vg0200456649 G -> C LOC_Os02g01825.1 missense_variant ; p.Ala249Gly; MODERATE nonsynonymous_codon ; A249G Average:49.272; most accessible tissue: Zhenshan97 flower, score: 70.756 benign 0.429 TOLERATED 0.42

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0200456649 NA 2.04E-12 mr1579 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
vg0200456649 NA 1.44E-07 mr1680 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
vg0200456649 NA 4.40E-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
vg0200456649 1.84E-06 5.77E-15 mr1349_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
vg0200456649 NA 1.48E-07 mr1349_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
vg0200456649 NA 9.82E-12 mr1377_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
vg0200456649 NA 7.02E-08 mr1568_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
vg0200456649 NA 2.86E-09 mr1576_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
vg0200456649 NA 1.57E-14 mr1666_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
vg0200456649 NA 4.37E-17 mr1712_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
vg0200456649 NA 1.29E-12 mr1761_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