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Detailed information for vg1227225397:

Variant ID: vg1227225397 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 27225397
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


AGCGGCCCAACAGCTTGTACCAACCGAGTGTGTGGACCTAGTAGAATTGGGCTGGGCCACAGTGAGGGAGAGAGGTCCATAGCTCATCGCTATAAGAGAC[C/T]
GGCAGGGAAGAGAACGAATCGAACATTGTAGAAACAAATATTTGGAAATCAATTCAAATCTCTCCCTGTTCTATTGCTGCCTCTACCTGTTCTTAGCTGT

Reverse complement sequence

ACAGCTAAGAACAGGTAGAGGCAGCAATAGAACAGGGAGAGATTTGAATTGATTTCCAAATATTTGTTTCTACAATGTTCGATTCGTTCTCTTCCCTGCC[G/A]
GTCTCTTATAGCGATGAGCTATGGACCTCTCTCCCTCACTGTGGCCCAGCCCAATTCTACTAGGTCCACACACTCGGTTGGTACAAGCTGTTGGGCCGCT

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 99.20% 0.60% 0.19% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 97.60% 1.90% 0.60% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 95.30% 3.70% 1.04% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg1227225397 C -> T LOC_Os12g43850.1 downstream_gene_variant ; 60.0bp to feature; MODIFIER silent_mutation Average:67.614; most accessible tissue: Callus, score: 86.379 N N N N
vg1227225397 C -> T LOC_Os12g43850-LOC_Os12g43860 intergenic_region ; MODIFIER silent_mutation Average:67.614; most accessible tissue: Callus, score: 86.379 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1227225397 3.59E-06 4.79E-09 mr1486 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
vg1227225397 NA 6.04E-06 mr1548 Jap_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
vg1227225397 1.49E-07 2.83E-10 mr1486_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
vg1227225397 NA 7.50E-06 mr1588_2 Jap_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