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Detailed information for vg0205588537:

Variant ID: vg0205588537 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5588537
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.02, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


ACTCACGGGCTGTAGCCAGATGCTTTTGCAAGTGCATCATATGAGTTCCAATTATGCTGTTTATTGACTAGAGAGAAAAACTTACATCAACAGAAAGAAC[C/T]
GCCGAGTAGACTTCTGACATTTTCACATCTTCATTGGCTAATAGAGAACCTTCTTCACAAGGGAGCTGTTTCAGTTCAGAATTTTTGTCAATCATCTCTC

Reverse complement sequence

GAGAGATGATTGACAAAAATTCTGAACTGAAACAGCTCCCTTGTGAAGAAGGTTCTCTATTAGCCAATGAAGATGTGAAAATGTCAGAAGTCTACTCGGC[G/A]
GTTCTTTCTGTTGATGTAAGTTTTTCTCTCTAGTCAATAAACAGCATAATTGGAACTCATATGATGCACTTGCAAAAGCATCTGGCTACAGCCCGTGAGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.20% 44.80% 0.06% 0.00% NA
All Indica  2759 88.60% 11.30% 0.07% 0.00% NA
All Japonica  1512 2.90% 97.00% 0.07% 0.00% NA
Aus  269 27.90% 72.10% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 70.30% 29.70% 0.00% 0.00% NA
Indica III  913 93.50% 6.50% 0.00% 0.00% NA
Indica Intermediate  786 85.10% 14.60% 0.25% 0.00% NA
Temperate Japonica  767 2.20% 97.80% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 9.10% 90.50% 0.41% 0.00% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 40.00% 60.00% 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
vg0205588537 C -> T LOC_Os02g10630.1 synonymous_variant ; p.Ala949Ala; LOW synonymous_codon Average:66.153; most accessible tissue: Callus, score: 85.966 N N N N
vg0205588537 C -> T LOC_Os02g10630.1 synonymous_variant ; p.Ala949Ala; LOW nonsynonymous_codon ; A949V Average:66.153; most accessible tissue: Callus, score: 85.966 benign 0.217 TOLERATED 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205588537 NA 1.08E-14 mr1032 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
vg0205588537 NA 8.34E-07 mr1032 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
vg0205588537 NA 3.23E-19 mr1077 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
vg0205588537 NA 1.27E-08 mr1170 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
vg0205588537 NA 1.51E-14 mr1478 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
vg0205588537 NA 3.39E-06 mr1478 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
vg0205588537 NA 8.83E-06 mr1553 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
vg0205588537 NA 9.99E-08 mr1836 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
vg0205588537 NA 1.83E-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
vg0205588537 NA 8.99E-19 mr1165_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
vg0205588537 NA 1.12E-06 mr1170_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
vg0205588537 4.47E-08 NA mr1180_2 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
vg0205588537 NA 3.34E-07 mr1321_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
vg0205588537 NA 4.63E-10 mr1478_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
vg0205588537 NA 8.58E-06 mr1648_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
vg0205588537 NA 4.28E-09 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
vg0205588537 NA 4.21E-07 mr1668_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