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Detailed information for vg1116285968:

Variant ID: vg1116285968 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 16285968
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.66, C: 0.34, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


CTAGCACCCAGGATAGTTTGATTAGGTTATGAACTACAGTTTCCTTTCACTAAAACTTGTTACCCTTCATCTTTTGCTTCTTTATACACTGCCCCACACC[T/C]
ACCAATTACCTTCAACAAAATTAACTATAAACAACAAAAAATAATATAGTTATAGTTATAAACTTGTTGCCCTTCATCTTTTGCTTCTTTATACACTGCC

Reverse complement sequence

GGCAGTGTATAAAGAAGCAAAAGATGAAGGGCAACAAGTTTATAACTATAACTATATTATTTTTTGTTGTTTATAGTTAATTTTGTTGAAGGTAATTGGT[A/G]
GGTGTGGGGCAGTGTATAAAGAAGCAAAAGATGAAGGGTAACAAGTTTTAGTGAAAGGAAACTGTAGTTCATAACCTAATCAAACTATCCTGGGTGCTAG

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 62.30% 34.40% 0.15% 3.20% NA
All Indica  2759 93.20% 1.80% 0.18% 4.82% NA
All Japonica  1512 3.40% 95.80% 0.07% 0.73% NA
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 94.10% 1.80% 0.00% 4.03% NA
Indica II  465 88.40% 0.20% 0.65% 10.75% NA
Indica III  913 99.50% 0.30% 0.00% 0.22% NA
Indica Intermediate  786 88.20% 4.30% 0.25% 7.25% NA
Temperate Japonica  767 1.20% 97.40% 0.13% 1.30% NA
Tropical Japonica  504 7.10% 92.70% 0.00% 0.20% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 8.30% 88.50% 1.04% 2.08% NA
Intermediate  90 55.60% 38.90% 0.00% 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
vg1116285968 T -> DEL N N silent_mutation Average:55.637; most accessible tissue: Zhenshan97 panicle, score: 81.752 N N N N
vg1116285968 T -> C LOC_Os11g28310.1 downstream_gene_variant ; 3243.0bp to feature; MODIFIER silent_mutation Average:55.637; most accessible tissue: Zhenshan97 panicle, score: 81.752 N N N N
vg1116285968 T -> C LOC_Os11g28310-LOC_Os11g28320 intergenic_region ; MODIFIER silent_mutation Average:55.637; most accessible tissue: Zhenshan97 panicle, score: 81.752 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1116285968 NA 4.11E-81 mr1134 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
vg1116285968 NA 5.09E-77 mr1135 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
vg1116285968 NA 2.59E-24 mr1375 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
vg1116285968 NA 5.13E-14 mr1376 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
vg1116285968 NA 3.90E-24 mr1383 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
vg1116285968 NA 5.13E-14 mr1431 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
vg1116285968 NA 1.59E-85 mr1504 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
vg1116285968 NA 3.97E-11 mr1553 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
vg1116285968 NA 9.07E-83 mr1672 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
vg1116285968 NA 7.50E-07 mr1690 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
vg1116285968 NA 4.02E-21 mr1698 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
vg1116285968 NA 3.21E-99 mr1758 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
vg1116285968 1.36E-06 1.36E-06 mr1050_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
vg1116285968 1.25E-07 3.43E-142 mr1758_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
vg1116285968 2.13E-06 2.80E-09 mr1758_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