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Detailed information for vg0201776356:

Variant ID: vg0201776356 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 1776356
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGTCAAATTATCAATCAAAAATAAAAATCAAACTAGTAGTATCATTTTTTAATGATTATGTAAGTTTGTTGATACTGCCACTATATTTAAATATATGA[C/T]
ACTGTTCACTTTATTTGGTCTTCGGCGTGCAACTTTGACCACTATTCTTCTATTAGAATAGAACGATAATATCTTCTTTTTTTATAATGTAGAATTACTT

Reverse complement sequence

AAGTAATTCTACATTATAAAAAAAGAAGATATTATCGTTCTATTCTAATAGAAGAATAGTGGTCAAAGTTGCACGCCGAAGACCAAATAAAGTGAACAGT[G/A]
TCATATATTTAAATATAGTGGCAGTATCAACAAACTTACATAATCATTAAAAAATGATACTACTAGTTTGATTTTTATTTTTGATTGATAATTTGACAAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.80% 6.10% 1.10% 0.00% NA
All Indica  2759 87.70% 10.40% 1.81% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 62.90% 30.40% 6.72% 0.00% NA
Indica II  465 96.80% 2.40% 0.86% 0.00% NA
Indica III  913 95.40% 4.60% 0.00% 0.00% NA
Indica Intermediate  786 92.40% 6.90% 0.76% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 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
vg0201776356 C -> T LOC_Os02g04070.1 downstream_gene_variant ; 3736.0bp to feature; MODIFIER silent_mutation Average:33.81; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N
vg0201776356 C -> T LOC_Os02g04090.1 downstream_gene_variant ; 4000.0bp to feature; MODIFIER silent_mutation Average:33.81; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N
vg0201776356 C -> T LOC_Os02g04080.1 intron_variant ; MODIFIER silent_mutation Average:33.81; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0201776356 8.83E-07 6.46E-06 mr1397 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
vg0201776356 NA 4.01E-06 mr1496 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
vg0201776356 NA 4.87E-06 mr1864 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
vg0201776356 NA 4.44E-06 mr1201_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