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Detailed information for vg1115981616:

Variant ID: vg1115981616 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 15981616
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: 96. )

Flanking Sequence (100 bp) in Reference Genome:


ATGAGATGAAATTGTCTGATTTAACAGCAATCAAGAAAAGACACGATGAACCTGTACTTGAGTATATTCAGAGGTTCAGAGAGATGTGGAATAAGTGCTA[C/T]
AGCTTGAGTTTGACTGATGCCCAGTTAGCCGATTTGGCTTTTCAGGGTATGATTGCTCCGATCAGGGAGAAATTCTCAGCTGAAGACTTTGACAGCTTGT

Reverse complement sequence

ACAAGCTGTCAAAGTCTTCAGCTGAGAATTTCTCCCTGATCGGAGCAATCATACCCTGAAAAGCCAAATCGGCTAACTGGGCATCAGTCAAACTCAAGCT[G/A]
TAGCACTTATTCCACATCTCTCTGAACCTCTGAATATACTCAAGTACAGGTTCATCGTGTCTTTTCTTGATTGCTGTTAAATCAGACAATTTCATCTCAT

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 49.70% 23.10% 27.04% 0.15% NA
All Indica  2759 23.40% 35.80% 40.59% 0.25% NA
All Japonica  1512 97.80% 0.50% 1.72% 0.00% NA
Aus  269 33.10% 29.00% 37.92% 0.00% NA
Indica I  595 19.50% 22.40% 57.65% 0.50% NA
Indica II  465 18.70% 38.10% 43.23% 0.00% NA
Indica III  913 26.90% 45.30% 27.60% 0.11% NA
Indica Intermediate  786 24.90% 33.50% 41.22% 0.38% NA
Temperate Japonica  767 97.50% 0.30% 2.22% 0.00% NA
Tropical Japonica  504 97.60% 0.80% 1.59% 0.00% NA
Japonica Intermediate  241 98.80% 0.80% 0.41% 0.00% NA
VI/Aromatic  96 92.70% 1.00% 6.25% 0.00% NA
Intermediate  90 55.60% 17.80% 26.67% 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
vg1115981616 C -> T LOC_Os11g27760.1 synonymous_variant ; p.Tyr384Tyr; LOW synonymous_codon Average:10.492; most accessible tissue: Callus, score: 28.482 N N N N
vg1115981616 C -> DEL LOC_Os11g27760.1 N frameshift_variant Average:10.492; most accessible tissue: Callus, score: 28.482 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1115981616 3.02E-06 NA mr1151_2 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
vg1115981616 NA 5.82E-08 mr1299_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
vg1115981616 NA 3.71E-11 mr1537_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
vg1115981616 NA 4.71E-08 mr1727_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
vg1115981616 NA 8.43E-07 mr1785_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
vg1115981616 NA 4.96E-08 mr1804_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
vg1115981616 NA 1.15E-07 mr1837_2 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
vg1115981616 NA 8.64E-06 mr1840_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
vg1115981616 NA 2.26E-06 mr1915_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