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Detailed information for vg0204550077:

Variant ID: vg0204550077 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4550077
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TCTGCATCTTCACTCTCATCGTCTGACGTGTCACTTGTATCTTCTATTAAGTAGTCCTCATGAGCATCACATCTCTCAAACTCCTTATCACGTAAATTGC[T/A]
ATCACGGACGAAGTTATGCATAGCAAGACAAGCCATGATGATATGCTTCTGAGTAGTAGGTGAGAAACTTGGGATGCCCTTCAAAATACGCCACTTTTGC

Reverse complement sequence

GCAAAAGTGGCGTATTTTGAAGGGCATCCCAAGTTTCTCACCTACTACTCAGAAGCATATCATCATGGCTTGTCTTGCTATGCATAACTTCGTCCGTGAT[A/T]
GCAATTTACGTGATAAGGAGTTTGAGAGATGTGATGCTCATGAGGACTACTTAATAGAAGATACAAGTGACACGTCAGACGATGAGAGTGAAGATGCAGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.60% 17.10% 0.28% 0.00% NA
All Indica  2759 74.60% 24.90% 0.43% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 59.50% 40.10% 0.37% 0.00% NA
Indica I  595 64.90% 33.80% 1.34% 0.00% NA
Indica II  465 73.30% 26.70% 0.00% 0.00% NA
Indica III  913 85.40% 14.60% 0.00% 0.00% NA
Indica Intermediate  786 70.20% 29.30% 0.51% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0204550077 T -> A LOC_Os02g08450.1 missense_variant ; p.Ser600Cys; MODERATE nonsynonymous_codon ; S600C Average:21.246; most accessible tissue: Minghui63 panicle, score: 38.588 probably damaging 3.175 DELETERIOUS 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0204550077 NA 6.11E-08 mr1850 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
vg0204550077 1.79E-06 1.79E-06 mr1850 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