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Detailed information for vg0200713263:

Variant ID: vg0200713263 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 713263
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.80, T: 0.19, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


TGTTTGACCGTTCGTCTTATTCAAAAAATTTTGTGGAATATGTAAAACTATACGTATATATATAAGTATATTTAACAATGAATCAAATGATAGGAAAAGA[A/T]
TTAATAATTACTTAAATTTTTTAAATAAGACGAATGGTCAAATATATTTAAAAAGGTTAACGGCATCAAATATTTAGAAAGGGATTGAATATTTCCACTC

Reverse complement sequence

GAGTGGAAATATTCAATCCCTTTCTAAATATTTGATGCCGTTAACCTTTTTAAATATATTTGACCATTCGTCTTATTTAAAAAATTTAAGTAATTATTAA[T/A]
TCTTTTCCTATCATTTGATTCATTGTTAAATATACTTATATATATACGTATAGTTTTACATATTCCACAAAATTTTTTGAATAAGACGAACGGTCAAACA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.00% 19.60% 0.34% 0.00% NA
All Indica  2759 91.60% 8.40% 0.04% 0.00% NA
All Japonica  1512 56.30% 42.90% 0.86% 0.00% NA
Aus  269 90.70% 8.90% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 77.00% 22.80% 0.22% 0.00% NA
Indica III  913 92.90% 7.10% 0.00% 0.00% NA
Indica Intermediate  786 92.40% 7.60% 0.00% 0.00% NA
Temperate Japonica  767 70.10% 28.70% 1.17% 0.00% NA
Tropical Japonica  504 30.60% 68.80% 0.60% 0.00% NA
Japonica Intermediate  241 66.00% 33.60% 0.41% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 76.70% 22.20% 1.11% 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
vg0200713263 A -> T LOC_Os02g02240.1 upstream_gene_variant ; 4594.0bp to feature; MODIFIER silent_mutation Average:39.233; most accessible tissue: Callus, score: 73.362 N N N N
vg0200713263 A -> T LOC_Os02g02230.1 intron_variant ; MODIFIER silent_mutation Average:39.233; most accessible tissue: Callus, score: 73.362 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0200713263 NA 2.45E-08 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
vg0200713263 5.36E-06 3.97E-10 mr1709 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
vg0200713263 2.64E-06 2.64E-06 mr1894 Jap_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
vg0200713263 NA 7.19E-07 mr1182_2 Jap_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