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Detailed information for vg0802090518:

Variant ID: vg0802090518 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 2090518
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, T: 0.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


TCCCTGCCGTACACGCACTAGTTGGCTATTTTTTATTATTATCTGAAGTCCTGTAACATAAATTATCTTTGTTGCAGGGACTGTTTTAACCTGTCCTTTT[A/T]
TGTTCTTTTTTTTATGTTCTGCTGTTTACTTTTCCCTGTTTTATTTTCATGCAGAAGTGGCATATGCAAACGTTCCTACAACTTCATATGAGCTTCCAGA

Reverse complement sequence

TCTGGAAGCTCATATGAAGTTGTAGGAACGTTTGCATATGCCACTTCTGCATGAAAATAAAACAGGGAAAAGTAAACAGCAGAACATAAAAAAAAGAACA[T/A]
AAAAGGACAGGTTAAAACAGTCCCTGCAACAAAGATAATTTATGTTACAGGACTTCAGATAATAATAAAAAATAGCCAACTAGTGCGTGTACGGCAGGGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.60% 5.00% 8.65% 3.77% NA
All Indica  2759 78.30% 0.90% 14.46% 6.38% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 24.50% 75.50% 0.00% 0.00% NA
Indica I  595 73.40% 0.00% 21.68% 4.87% NA
Indica II  465 77.40% 0.20% 16.99% 5.38% NA
Indica III  913 81.20% 0.50% 8.76% 9.53% NA
Indica Intermediate  786 79.10% 2.30% 14.12% 4.45% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 4.20% 3.12% 0.00% NA
Intermediate  90 84.40% 5.60% 7.78% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0802090518 A -> T LOC_Os08g04280.1 intron_variant ; MODIFIER silent_mutation Average:39.669; most accessible tissue: Callus, score: 68.868 N N N N
vg0802090518 A -> T LOC_Os08g04280.2 intron_variant ; MODIFIER silent_mutation Average:39.669; most accessible tissue: Callus, score: 68.868 N N N N
vg0802090518 A -> DEL N N silent_mutation Average:39.669; most accessible tissue: Callus, score: 68.868 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0802090518 6.83E-06 NA mr1113 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
vg0802090518 1.59E-06 NA mr1114 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
vg0802090518 2.23E-06 NA mr1117 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
vg0802090518 4.34E-06 NA mr1119 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
vg0802090518 1.52E-09 NA mr1123 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
vg0802090518 3.22E-06 NA mr1240 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
vg0802090518 1.84E-07 NA mr1496 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
vg0802090518 4.77E-06 NA mr1242_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