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Detailed information for vg0200970312:

Variant ID: vg0200970312 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 970312
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.02, G: 0.00, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


AATTTAGTTGATTGGGGCTTCTTTGAAGAGGTTGAGTCACACTATGTTATGCATGACCTAATGCATGACTTGGCAGAAGAAGTTTCATCAGATGAGTGTG[A/C]
TACTGTAGATGGATTGGAATCCAAGAAAATTTCACCAGGTCTTCAGCATTTATCAATAATAACTACTGCTTATGATAGAGAAGAACCTTGCAATTTTCCT

Reverse complement sequence

AGGAAAATTGCAAGGTTCTTCTCTATCATAAGCAGTAGTTATTATTGATAAATGCTGAAGACCTGGTGAAATTTTCTTGGATTCCAATCCATCTACAGTA[T/G]
CACACTCATCTGATGAAACTTCTTCTGCCAAGTCATGCATTAGGTCATGCATAACATAGTGTGACTCAACCTCTTCAAAGAAGCCCCAATCAACTAAATT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.10% 40.10% 2.88% 0.00% NA
All Indica  2759 87.80% 7.40% 4.82% 0.00% NA
All Japonica  1512 4.60% 95.30% 0.07% 0.00% NA
Aus  269 59.10% 40.90% 0.00% 0.00% NA
Indica I  595 92.30% 2.00% 5.71% 0.00% NA
Indica II  465 72.50% 23.90% 3.66% 0.00% NA
Indica III  913 92.70% 1.30% 6.02% 0.00% NA
Indica Intermediate  786 87.90% 8.70% 3.44% 0.00% NA
Temperate Japonica  767 0.40% 99.50% 0.13% 0.00% NA
Tropical Japonica  504 6.90% 93.10% 0.00% 0.00% NA
Japonica Intermediate  241 13.30% 86.70% 0.00% 0.00% NA
VI/Aromatic  96 15.60% 84.40% 0.00% 0.00% NA
Intermediate  90 33.30% 64.40% 2.22% 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
vg0200970312 A -> C LOC_Os02g02640.1 missense_variant ; p.Asp537Ala; MODERATE nonsynonymous_codon ; D537A Average:47.735; most accessible tissue: Callus, score: 75.454 benign -0.285 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0200970312 NA 2.53E-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
vg0200970312 NA 3.98E-10 mr1050_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
vg0200970312 NA 2.49E-06 mr1074_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
vg0200970312 NA 2.68E-32 mr1081_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
vg0200970312 NA 1.32E-15 mr1148_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
vg0200970312 NA 2.76E-06 mr1148_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
vg0200970312 NA 1.71E-07 mr1150_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
vg0200970312 NA 4.14E-07 mr1227_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
vg0200970312 NA 8.19E-08 mr1272_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
vg0200970312 NA 6.54E-06 mr1272_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
vg0200970312 NA 4.64E-10 mr1660_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
vg0200970312 6.64E-06 6.89E-08 mr1660_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
vg0200970312 NA 1.02E-10 mr1835_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
vg0200970312 NA 8.89E-06 mr1835_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
vg0200970312 NA 2.84E-06 mr1871_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
vg0200970312 NA 1.32E-14 mr1904_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
vg0200970312 NA 1.57E-08 mr1940_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