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Detailed information for vg1200762080:

Variant ID: vg1200762080 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 762080
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.02, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


AATGGCTATTTAGGTGGGGGGCATGAAAGCAACAATGAGATATTTCTCGAGATATGAAACATTTTCCCATAAAATAACTAACTTTCTATATATGTGCATT[T/A]
TTTTCTTTGGTGCAGGGTCAGTTAAATCAATCCTGCTTGGATCGATCGATCGAGCTTAACATGCTAGCTCAATCGGAGTTGATCAGCTAGTAATTAAGCA

Reverse complement sequence

TGCTTAATTACTAGCTGATCAACTCCGATTGAGCTAGCATGTTAAGCTCGATCGATCGATCCAAGCAGGATTGATTTAACTGACCCTGCACCAAAGAAAA[A/T]
AATGCACATATATAGAAAGTTAGTTATTTTATGGGAAAATGTTTCATATCTCGAGAAATATCTCATTGTTGCTTTCATGCCCCCCACCTAAATAGCCATT

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 92.60% 7.40% 0.06% 0.00% NA
All Indica  2759 87.40% 12.50% 0.11% 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 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 71.70% 27.90% 0.33% 0.00% NA
Indica Intermediate  786 89.90% 10.10% 0.00% 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 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg1200762080 T -> A LOC_Os12g02350.1 upstream_gene_variant ; 1711.0bp to feature; MODIFIER silent_mutation Average:38.354; most accessible tissue: Zhenshan97 flower, score: 78.5 N N N N
vg1200762080 T -> A LOC_Os12g02370.2 downstream_gene_variant ; 4354.0bp to feature; MODIFIER silent_mutation Average:38.354; most accessible tissue: Zhenshan97 flower, score: 78.5 N N N N
vg1200762080 T -> A LOC_Os12g02370.4 downstream_gene_variant ; 4354.0bp to feature; MODIFIER silent_mutation Average:38.354; most accessible tissue: Zhenshan97 flower, score: 78.5 N N N N
vg1200762080 T -> A LOC_Os12g02340.1 intron_variant ; MODIFIER silent_mutation Average:38.354; most accessible tissue: Zhenshan97 flower, score: 78.5 N N N N
vg1200762080 T -> A LOC_Os12g02340.2 intron_variant ; MODIFIER silent_mutation Average:38.354; most accessible tissue: Zhenshan97 flower, score: 78.5 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1200762080 NA 9.37E-06 mr1086 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
vg1200762080 NA 7.31E-06 mr1107 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
vg1200762080 NA 1.42E-07 mr1244 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
vg1200762080 NA 3.23E-06 mr1973 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