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Detailed information for vg1219400490:

Variant ID: vg1219400490 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 19400490
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.02, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TACACGCGTGATTTTCTCTGCATCGGTTATTGTTTGACCATCCAATATGTACCAGCCATGCGGGCAGCTGAGCCATTCGTATATATGGTTATTAATTTAA[G/T]
TGTGTGCAAGGTGTTCCATTCTGATCGGCACCGCAGCATGACCGGCGCCATAGAAGTGGCCCTGATTCAATAGCTTGGGAACTCTTGTAGGAGATGAAGA

Reverse complement sequence

TCTTCATCTCCTACAAGAGTTCCCAAGCTATTGAATCAGGGCCACTTCTATGGCGCCGGTCATGCTGCGGTGCCGATCAGAATGGAACACCTTGCACACA[C/A]
TTAAATTAATAACCATATATACGAATGGCTCAGCTGCCCGCATGGCTGGTACATATTGGATGGTCAAACAATAACCGATGCAGAGAAAATCACGCGTGTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 71.10% 28.80% 0.11% 0.00% NA
All Indica  2759 51.80% 48.00% 0.18% 0.00% NA
All Japonica  1512 99.10% 0.90% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 59.70% 40.20% 0.17% 0.00% NA
Indica II  465 81.50% 18.50% 0.00% 0.00% NA
Indica III  913 31.10% 68.70% 0.22% 0.00% NA
Indica Intermediate  786 52.30% 47.50% 0.25% 0.00% NA
Temperate Japonica  767 99.20% 0.80% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg1219400490 G -> T LOC_Os12g32160.1 downstream_gene_variant ; 4698.0bp to feature; MODIFIER silent_mutation Average:35.575; most accessible tissue: Callus, score: 65.574 N N N N
vg1219400490 G -> T LOC_Os12g32150-LOC_Os12g32160 intergenic_region ; MODIFIER silent_mutation Average:35.575; most accessible tissue: Callus, score: 65.574 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1219400490 5.76E-08 NA mr1458 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
vg1219400490 2.85E-06 NA mr1458 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
vg1219400490 3.37E-06 NA mr1458_2 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
vg1219400490 4.02E-06 NA mr1458_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