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Detailed information for vg1119344818:

Variant ID: vg1119344818 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 19344818
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


ACCATTACCATGCCTGCATAGAAGCTCTTTTGCGGAGAGGAGGTGGAGAGGAAAAGGAGGGGCGAAGAAGGAGAGGCGGAAGAGGAGGATAACGAAGGAT[C/T]
TGGAAGAGAAAGAAAAAAAAGAATGGGAACGGATAAGAGTAAAACGTTATCCACTTATCCCGTATCTACGGGATACTATATGGTAGATTTTCTGAAAATA

Reverse complement sequence

TATTTTCAGAAAATCTACCATATAGTATCCCGTAGATACGGGATAAGTGGATAACGTTTTACTCTTATCCGTTCCCATTCTTTTTTTTCTTTCTCTTCCA[G/A]
ATCCTTCGTTATCCTCCTCTTCCGCCTCTCCTTCTTCGCCCCTCCTTTTCCTCTCCACCTCCTCTCCGCAAAAGAGCTTCTATGCAGGCATGGTAATGGT

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 95.20% 4.80% 0.00% 0.00% NA
All Indica  2759 96.10% 3.90% 0.00% 0.00% NA
All Japonica  1512 96.20% 3.80% 0.00% 0.00% NA
Aus  269 77.70% 22.30% 0.00% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 91.60% 8.40% 0.00% 0.00% NA
Indica III  913 98.50% 1.50% 0.00% 0.00% NA
Indica Intermediate  786 94.30% 5.70% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 92.70% 7.30% 0.00% 0.00% NA
Japonica Intermediate  241 92.10% 7.90% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1119344818 C -> T LOC_Os11g32740.1 upstream_gene_variant ; 4182.0bp to feature; MODIFIER silent_mutation Average:47.762; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg1119344818 C -> T LOC_Os11g32720-LOC_Os11g32740 intergenic_region ; MODIFIER silent_mutation Average:47.762; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1119344818 NA 1.10E-06 mr1354 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
vg1119344818 NA 1.10E-08 mr1546 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
vg1119344818 2.83E-06 1.99E-06 mr1651 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
vg1119344818 NA 2.44E-08 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