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Detailed information for vg1211686189:

Variant ID: vg1211686189 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 11686189
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


CTCACTAGTAAATCCTCTCTATCCTGGCCTATCAATTGCTTGGTGTCCTTGGATGAACCGGAGGAAGCTCTGATCACACATGTTCCCTTGGATTCGATAC[C/T,A]
CTTGGAATACTCCGTAGGGGAAGTGCTACATCGGTATATCCGTGCGCTTGCGGATTTTATCTGTAACCGTATCAAATACCAACACTAGACTCAGATCAGC

Reverse complement sequence

GCTGATCTGAGTCTAGTGTTGGTATTTGATACGGTTACAGATAAAATCCGCAAGCGCACGGATATACCGATGTAGCACTTCCCCTACGGAGTATTCCAAG[G/A,T]
GTATCGAATCCAAGGGAACATGTGTGATCAGAGCTTCCTCCGGTTCATCCAAGGACACCAAGCAATTGATAGGCCAGGATAGAGAGGATTTACTAGTGAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.50% 2.80% 2.48% 2.96% T: 0.28%
All Indica  2759 97.40% 0.00% 1.81% 0.36% T: 0.43%
All Japonica  1512 81.50% 6.70% 3.24% 8.47% NA
Aus  269 87.40% 7.40% 4.83% 0.00% T: 0.37%
Indica I  595 97.80% 0.00% 2.02% 0.17% NA
Indica II  465 95.50% 0.20% 3.23% 0.65% T: 0.43%
Indica III  913 98.70% 0.00% 0.44% 0.22% T: 0.66%
Indica Intermediate  786 96.60% 0.00% 2.42% 0.51% T: 0.51%
Temperate Japonica  767 85.90% 1.30% 1.83% 10.95% NA
Tropical Japonica  504 75.80% 14.10% 4.17% 5.95% NA
Japonica Intermediate  241 79.70% 8.70% 5.81% 5.81% NA
VI/Aromatic  96 91.70% 4.20% 4.17% 0.00% NA
Intermediate  90 93.30% 3.30% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1211686189 C -> DEL N N silent_mutation Average:27.987; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 N N N N
vg1211686189 C -> A LOC_Os12g20110.1 upstream_gene_variant ; 4022.0bp to feature; MODIFIER silent_mutation Average:27.987; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 N N N N
vg1211686189 C -> A LOC_Os12g20100.1 downstream_gene_variant ; 419.0bp to feature; MODIFIER silent_mutation Average:27.987; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 N N N N
vg1211686189 C -> A LOC_Os12g20090-LOC_Os12g20100 intergenic_region ; MODIFIER silent_mutation Average:27.987; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 N N N N
vg1211686189 C -> T LOC_Os12g20110.1 upstream_gene_variant ; 4022.0bp to feature; MODIFIER silent_mutation Average:27.987; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 N N N N
vg1211686189 C -> T LOC_Os12g20100.1 downstream_gene_variant ; 419.0bp to feature; MODIFIER silent_mutation Average:27.987; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 N N N N
vg1211686189 C -> T LOC_Os12g20090-LOC_Os12g20100 intergenic_region ; MODIFIER silent_mutation Average:27.987; most accessible tissue: Zhenshan97 flag leaf, score: 59.429 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1211686189 NA 8.58E-07 mr1531_2 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