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Detailed information for vg1109779912:

Variant ID: vg1109779912 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 9779912
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


CTTATCCAATCTGACCCGGACTTAGCCGATCCCGATCGTAGCCGATTTGGACTCCAGCCGATTCTTATTCTGTTCCCGAATCGATCTTCGTCTTTGATTC[C/T]
GCTTCGATCTAATTTTCATTTTCGATACTAGATATTACCAAATTTGGTCGTTAACAATTATATAATATAAATATTTCTCAATTTTTCCTCAATTGTCTCG

Reverse complement sequence

CGAGACAATTGAGGAAAAATTGAGAAATATTTATATTATATAATTGTTAACGACCAAATTTGGTAATATCTAGTATCGAAAATGAAAATTAGATCGAAGC[G/A]
GAATCAAAGACGAAGATCGATTCGGGAACAGAATAAGAATCGGCTGGAGTCCAAATCGGCTACGATCGGGATCGGCTAAGTCCGGGTCAGATTGGATAAG

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 75.60% 24.40% 0.04% 0.00% NA
All Indica  2759 68.00% 31.90% 0.07% 0.00% NA
All Japonica  1512 99.20% 0.80% 0.00% 0.00% NA
Aus  269 17.10% 82.90% 0.00% 0.00% NA
Indica I  595 85.50% 14.50% 0.00% 0.00% NA
Indica II  465 68.80% 31.00% 0.22% 0.00% NA
Indica III  913 53.30% 46.70% 0.00% 0.00% NA
Indica Intermediate  786 71.20% 28.60% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 98.00% 2.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 71.10% 28.90% 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
vg1109779912 C -> T LOC_Os11g17540.1 downstream_gene_variant ; 2872.0bp to feature; MODIFIER silent_mutation Average:31.71; most accessible tissue: Zhenshan97 young leaf, score: 58.398 N N N N
vg1109779912 C -> T LOC_Os11g17560.1 downstream_gene_variant ; 312.0bp to feature; MODIFIER silent_mutation Average:31.71; most accessible tissue: Zhenshan97 young leaf, score: 58.398 N N N N
vg1109779912 C -> T LOC_Os11g17540-LOC_Os11g17560 intergenic_region ; MODIFIER silent_mutation Average:31.71; most accessible tissue: Zhenshan97 young leaf, score: 58.398 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1109779912 NA 2.29E-06 mr1154 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
vg1109779912 6.32E-08 3.29E-11 mr1097_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
vg1109779912 NA 4.34E-07 mr1102_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
vg1109779912 1.52E-06 1.35E-08 mr1154_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