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Detailed information for vg1125735290:

Variant ID: vg1125735290 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25735290
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, C: 0.32, others allele: 0.00, population size: 136. )

Flanking Sequence (100 bp) in Reference Genome:


AGCTCCCTGAAACATCTCAAATGTCAATGCTTAAGGTGTTAGATCTAGAAGGTTGTCAATGCTTCCAGAGGAACCAGCACTACCTCAAGGACATTTGCAA[C/T]
AATATTTTACTGCTCAAGTATTTGAGCCTAAGGAGAACAGATGTTACACAGCTACCTAGTGAAATCAACAACCTCTATGAGCTGGAGGTACTGGATATTT

Reverse complement sequence

AAATATCCAGTACCTCCAGCTCATAGAGGTTGTTGATTTCACTAGGTAGCTGTGTAACATCTGTTCTCCTTAGGCTCAAATACTTGAGCAGTAAAATATT[G/A]
TTGCAAATGTCCTTGAGGTAGTGCTGGTTCCTCTGGAAGCATTGACAACCTTCTAGATCTAACACCTTAAGCATTGACATTTGAGATGTTTCAGGGAGCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.00% 28.70% 4.06% 13.22% NA
All Indica  2759 49.00% 29.90% 5.55% 15.59% NA
All Japonica  1512 61.60% 27.30% 1.39% 9.66% NA
Aus  269 46.80% 33.80% 5.20% 14.13% NA
Indica I  595 38.50% 44.70% 4.87% 11.93% NA
Indica II  465 56.60% 34.20% 3.01% 6.24% NA
Indica III  913 53.60% 20.60% 4.82% 21.03% NA
Indica Intermediate  786 47.10% 27.00% 8.40% 17.56% NA
Temperate Japonica  767 40.00% 44.70% 1.96% 13.30% NA
Tropical Japonica  504 88.50% 6.00% 0.99% 4.56% NA
Japonica Intermediate  241 74.30% 16.60% 0.41% 8.71% NA
VI/Aromatic  96 95.80% 0.00% 1.04% 3.12% NA
Intermediate  90 56.70% 31.10% 3.33% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125735290 C -> T LOC_Os11g42720.1 synonymous_variant ; p.Asn825Asn; LOW synonymous_codon Average:18.636; most accessible tissue: Callus, score: 49.019 N N N N
vg1125735290 C -> DEL LOC_Os11g42720.1 N frameshift_variant Average:18.636; most accessible tissue: Callus, score: 49.019 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125735290 NA 2.04E-08 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
vg1125735290 5.04E-06 3.65E-07 mr1569 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
vg1125735290 NA 1.23E-08 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
vg1125735290 2.49E-06 2.37E-12 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
vg1125735290 NA 1.86E-06 mr1835 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
vg1125735290 9.49E-07 2.42E-16 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
vg1125735290 NA 4.00E-06 mr1609_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
vg1125735290 NA 2.13E-06 mr1745_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
vg1125735290 5.65E-06 NA mr1900_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
vg1125735290 NA 2.03E-06 mr1900_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