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Detailed information for vg0612033836:

Variant ID: vg0612033836 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 12033836
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACATGGCTGCATCACTAAACGAAGAAATAGCACGAACTGGTACAAGATTTGTTAGCTACGAGTCACCCGATCGAACACCGTGTGCGCACACTGCATACGT[C/T]
GGGCACGGCAACAGACGAGAAAACTGAAGAACGCAGAAAAGGAATTCAGAACAGAGAAAGCAAAGTTTTACTGAGTTTCAGAACTTCGCGAGAGAGAGAG

Reverse complement sequence

CTCTCTCTCTCGCGAAGTTCTGAAACTCAGTAAAACTTTGCTTTCTCTGTTCTGAATTCCTTTTCTGCGTTCTTCAGTTTTCTCGTCTGTTGCCGTGCCC[G/A]
ACGTATGCAGTGTGCGCACACGGTGTTCGATCGGGTGACTCGTAGCTAACAAATCTTGTACCAGTTCGTGCTATTTCTTCGTTTAGTGATGCAGCCATGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.70% 33.20% 0.08% 0.00% NA
All Indica  2759 95.00% 4.90% 0.07% 0.00% NA
All Japonica  1512 11.20% 88.80% 0.07% 0.00% NA
Aus  269 89.60% 10.40% 0.00% 0.00% NA
Indica I  595 94.10% 5.70% 0.17% 0.00% NA
Indica II  465 96.60% 3.20% 0.22% 0.00% NA
Indica III  913 96.50% 3.50% 0.00% 0.00% NA
Indica Intermediate  786 93.00% 7.00% 0.00% 0.00% NA
Temperate Japonica  767 3.30% 96.70% 0.00% 0.00% NA
Tropical Japonica  504 24.40% 75.40% 0.20% 0.00% NA
Japonica Intermediate  241 8.70% 91.30% 0.00% 0.00% NA
VI/Aromatic  96 68.80% 31.20% 0.00% 0.00% NA
Intermediate  90 60.00% 38.90% 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
vg0612033836 C -> T LOC_Os06g20840.1 downstream_gene_variant ; 656.0bp to feature; MODIFIER silent_mutation Average:44.62; most accessible tissue: Zhenshan97 young leaf, score: 69.263 N N N N
vg0612033836 C -> T LOC_Os06g20850.1 downstream_gene_variant ; 3880.0bp to feature; MODIFIER silent_mutation Average:44.62; most accessible tissue: Zhenshan97 young leaf, score: 69.263 N N N N
vg0612033836 C -> T LOC_Os06g20830-LOC_Os06g20840 intergenic_region ; MODIFIER silent_mutation Average:44.62; most accessible tissue: Zhenshan97 young leaf, score: 69.263 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0612033836 NA 3.47E-11 mr1138 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
vg0612033836 1.94E-06 NA mr1176 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
vg0612033836 1.96E-08 NA mr1033_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
vg0612033836 5.89E-07 NA mr1033_2 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
vg0612033836 6.09E-08 NA mr1087_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