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Detailed information for vg0218432703:

Variant ID: vg0218432703 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 18432703
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGTAGCGAGAGAAATCTCTTAAGGTTTAACACTTAGGTATTGATCTCTATTTATAGCCACTGCAGGGGAAACCGACACTAGGGTATGGCGGTTATCCCC[C/T]
GATCAGGGATGTTCATGAGAGATCGATCACTGTAGCGATCGCCCTAAACAAAATATCTCTTTGCCGACTTTAGGTTTAGCCGCAAGATCATATTTTGTGT

Reverse complement sequence

ACACAAAATATGATCTTGCGGCTAAACCTAAAGTCGGCAAAGAGATATTTTGTTTAGGGCGATCGCTACAGTGATCGATCTCTCATGAACATCCCTGATC[G/A]
GGGGATAACCGCCATACCCTAGTGTCGGTTTCCCCTGCAGTGGCTATAAATAGAGATCAATACCTAAGTGTTAAACCTTAAGAGATTTCTCTCGCTACCC

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 79.60% 17.80% 2.58% 0.00% NA
All Indica  2759 68.00% 28.00% 4.02% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 74.70% 21.60% 3.72% 0.00% NA
Indica I  595 77.50% 20.30% 2.18% 0.00% NA
Indica II  465 88.40% 9.20% 2.37% 0.00% NA
Indica III  913 43.50% 49.50% 7.01% 0.00% NA
Indica Intermediate  786 77.20% 19.80% 2.93% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 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 88.90% 10.00% 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
vg0218432703 C -> T LOC_Os02g30880.1 upstream_gene_variant ; 197.0bp to feature; MODIFIER silent_mutation Average:29.943; most accessible tissue: Zhenshan97 panicle, score: 43.098 N N N N
vg0218432703 C -> T LOC_Os02g30890.1 downstream_gene_variant ; 2399.0bp to feature; MODIFIER silent_mutation Average:29.943; most accessible tissue: Zhenshan97 panicle, score: 43.098 N N N N
vg0218432703 C -> T LOC_Os02g30880-LOC_Os02g30890 intergenic_region ; MODIFIER silent_mutation Average:29.943; most accessible tissue: Zhenshan97 panicle, score: 43.098 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0218432703 NA 3.02E-07 mr1138 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
vg0218432703 2.49E-07 NA mr1138_2 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
vg0218432703 9.42E-07 4.90E-07 mr1138_2 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
vg0218432703 NA 6.51E-07 mr1354_2 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