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Detailed information for vg1005630402:

Variant ID: vg1005630402 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5630402
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.80, A: 0.20, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


TATCCAAAGCATCAAAAGATAGAAGGACGATTACCATAACGCCACCCAAAACATACAACTTTCTTGTGTCAAAATATTCTTGTCCTTCTTCGTCTTTTTT[A/T]
TATATATATATTTTTGATTTCTTCACAACTCCTTTTTTACAACCTCTCTCTCTCTTTTTTACTTTTTTTTAACATGAAGCAACAAACATGAAACAATACA

Reverse complement sequence

TGTATTGTTTCATGTTTGTTGCTTCATGTTAAAAAAAAGTAAAAAAGAGAGAGAGAGGTTGTAAAAAAGGAGTTGTGAAGAAATCAAAAATATATATATA[T/A]
AAAAAAGACGAAGAAGGACAAGAATATTTTGACACAAGAAAGTTGTATGTTTTGGGTGGCGTTATGGTAATCGTCCTTCTATCTTTTGATGCTTTGGATA

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 92.50% 7.50% 0.02% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 81.30% 18.70% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.60% 1.40% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 84.00% 15.90% 0.13% 0.00% NA
Tropical Japonica  504 74.40% 25.60% 0.00% 0.00% NA
Japonica Intermediate  241 87.10% 12.90% 0.00% 0.00% NA
VI/Aromatic  96 58.30% 41.70% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg1005630402 A -> T LOC_Os10g10244.1 upstream_gene_variant ; 1845.0bp to feature; MODIFIER silent_mutation Average:38.233; most accessible tissue: Zhenshan97 young leaf, score: 52.657 N N N N
vg1005630402 A -> T LOC_Os10g10230.1 downstream_gene_variant ; 1293.0bp to feature; MODIFIER silent_mutation Average:38.233; most accessible tissue: Zhenshan97 young leaf, score: 52.657 N N N N
vg1005630402 A -> T LOC_Os10g10230-LOC_Os10g10244 intergenic_region ; MODIFIER silent_mutation Average:38.233; most accessible tissue: Zhenshan97 young leaf, score: 52.657 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005630402 8.70E-07 NA mr1768 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