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Detailed information for vg1125557272:

Variant ID: vg1125557272 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25557272
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


CATGACTTCATGTCAATGTCCTATGAATCTAAAACTTGAAGAGAGAAGCTCTGTTTAGTTCTAAATTTTTTTTTTCCAAACTTTCAACTTTTCATCACAT[C/T]
AAACCTTTCATACACACACAACTTTTCTATCACATCGTACCAATTTCAACTAAACTTCCAAACTTCAGTGTGAACTAAACATAGTCTCAGTGTAAAATTT

Reverse complement sequence

AAATTTTACACTGAGACTATGTTTAGTTCACACTGAAGTTTGGAAGTTTAGTTGAAATTGGTACGATGTGATAGAAAAGTTGTGTGTGTATGAAAGGTTT[G/A]
ATGTGATGAAAAGTTGAAAGTTTGGAAAAAAAAAATTTAGAACTAAACAGAGCTTCTCTCTTCAAGTTTTAGATTCATAGGACATTGACATGAAGTCATG

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 86.60% 10.60% 0.19% 2.58% NA
All Indica  2759 83.80% 14.60% 0.11% 1.56% NA
All Japonica  1512 93.00% 6.00% 0.07% 0.93% NA
Aus  269 92.60% 0.00% 0.00% 7.43% NA
Indica I  595 97.60% 0.80% 0.17% 1.34% NA
Indica II  465 80.90% 18.50% 0.00% 0.65% NA
Indica III  913 78.80% 18.90% 0.22% 2.08% NA
Indica Intermediate  786 80.80% 17.60% 0.00% 1.65% NA
Temperate Japonica  767 98.30% 0.50% 0.00% 1.17% NA
Tropical Japonica  504 84.50% 15.10% 0.00% 0.40% NA
Japonica Intermediate  241 93.80% 4.60% 0.41% 1.24% NA
VI/Aromatic  96 55.20% 0.00% 3.12% 41.67% NA
Intermediate  90 84.40% 7.80% 2.22% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125557272 C -> T LOC_Os11g42450.1 downstream_gene_variant ; 3717.0bp to feature; MODIFIER silent_mutation Average:64.435; most accessible tissue: Callus, score: 89.631 N N N N
vg1125557272 C -> T LOC_Os11g42450-LOC_Os11g42470 intergenic_region ; MODIFIER silent_mutation Average:64.435; most accessible tissue: Callus, score: 89.631 N N N N
vg1125557272 C -> DEL N N silent_mutation Average:64.435; most accessible tissue: Callus, score: 89.631 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125557272 6.04E-06 NA mr1133 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
vg1125557272 1.96E-06 2.10E-07 mr1191 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
vg1125557272 1.14E-06 NA mr1644 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
vg1125557272 2.17E-07 6.98E-09 mr1644 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
vg1125557272 9.89E-08 4.92E-13 mr1662 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
vg1125557272 NA 2.28E-07 mr1662 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
vg1125557272 NA 6.86E-07 mr1133_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
vg1125557272 4.21E-06 NA mr1191_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
vg1125557272 6.67E-06 2.65E-06 mr1191_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
vg1125557272 1.71E-06 2.81E-09 mr1662_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
vg1125557272 NA 7.67E-06 mr1850_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