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Detailed information for vg0207984549:

Variant ID: vg0207984549 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 7984549
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.66, T: 0.34, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


AGAGGTACTATATTTTATCGTGTAAAATTTGGTATCTCTCAGTACCTGTTATACTAGAAGCTAGGTAATTTGTACTAGAAATTGGTACCTCTTGGTACAC[T/C]
GTAAAATTTAATTTCTCTTTACAGTAAGAAACGAGGAGGACCTATAGTTTGCCCGACCGCATCGGGATGCACTCATGTGTAATCCTTATCCATGGTTTCC

Reverse complement sequence

GGAAACCATGGATAAGGATTACACATGAGTGCATCCCGATGCGGTCGGGCAAACTATAGGTCCTCCTCGTTTCTTACTGTAAAGAGAAATTAAATTTTAC[A/G]
GTGTACCAAGAGGTACCAATTTCTAGTACAAATTACCTAGCTTCTAGTATAACAGGTACTGAGAGATACCAAATTTTACACGATAAAATATAGTACCTCT

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 59.70% 39.80% 0.51% 0.00% NA
All Indica  2759 88.40% 10.80% 0.80% 0.00% NA
All Japonica  1512 2.80% 97.20% 0.00% 0.00% NA
Aus  269 88.50% 11.50% 0.00% 0.00% NA
Indica I  595 97.50% 1.50% 1.01% 0.00% NA
Indica II  465 86.90% 12.00% 1.08% 0.00% NA
Indica III  913 84.20% 15.40% 0.33% 0.00% NA
Indica Intermediate  786 87.30% 11.70% 1.02% 0.00% NA
Temperate Japonica  767 1.70% 98.30% 0.00% 0.00% NA
Tropical Japonica  504 4.20% 95.80% 0.00% 0.00% NA
Japonica Intermediate  241 3.30% 96.70% 0.00% 0.00% NA
VI/Aromatic  96 59.40% 40.60% 0.00% 0.00% NA
Intermediate  90 50.00% 47.80% 2.22% 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
vg0207984549 T -> C LOC_Os02g14490.1 upstream_gene_variant ; 1281.0bp to feature; MODIFIER silent_mutation Average:54.893; most accessible tissue: Callus, score: 88.57 N N N N
vg0207984549 T -> C LOC_Os02g14480-LOC_Os02g14490 intergenic_region ; MODIFIER silent_mutation Average:54.893; most accessible tissue: Callus, score: 88.57 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0207984549 NA 1.29E-09 mr1198 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
vg0207984549 NA 6.79E-18 mr1529 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
vg0207984549 NA 3.61E-14 mr1641 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
vg0207984549 NA 1.15E-08 mr1750 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
vg0207984549 NA 6.87E-34 mr1932 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
vg0207984549 NA 6.59E-19 mr1383_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
vg0207984549 7.56E-08 NA mr1750_2 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
vg0207984549 NA 2.36E-66 mr1828_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