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Detailed information for vg0906798732:

Variant ID: vg0906798732 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6798732
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


CATTCGACCATGGTGTCATATCACTCAATGCTTGAGTAGGAATTACCTACTGGATGATTATGTTATAAAAATTGTCTTTCATATAGACTTGACTAGCTGA[A/G]
TTCGGAAGAACACCATAAGAGAAGAATTCTTTGTACTCGGGATTGGCTGACATCCTCAGTGTATTTGGGAATGTCCATGATTAAAGATTAATTTGGTTTT

Reverse complement sequence

AAAACCAAATTAATCTTTAATCATGGACATTCCCAAATACACTGAGGATGTCAGCCAATCCCGAGTACAAAGAATTCTTCTCTTATGGTGTTCTTCCGAA[T/C]
TCAGCTAGTCAAGTCTATATGAAAGACAATTTTTATAACATAATCATCCAGTAGGTAATTCCTACTCAAGCATTGAGTGATATGACACCATGGTCGAATG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.20% 14.30% 0.04% 0.47% NA
All Indica  2759 82.50% 17.50% 0.07% 0.00% NA
All Japonica  1512 88.30% 11.70% 0.00% 0.00% NA
Aus  269 89.60% 2.60% 0.00% 7.81% NA
Indica I  595 95.30% 4.70% 0.00% 0.00% NA
Indica II  465 97.00% 3.00% 0.00% 0.00% NA
Indica III  913 63.90% 36.00% 0.11% 0.00% NA
Indica Intermediate  786 85.80% 14.10% 0.13% 0.00% NA
Temperate Japonica  767 95.80% 4.20% 0.00% 0.00% NA
Tropical Japonica  504 86.70% 13.30% 0.00% 0.00% NA
Japonica Intermediate  241 67.60% 32.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 91.10% 8.90% 0.00% 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
vg0906798732 A -> G LOC_Os09g12050.1 upstream_gene_variant ; 4529.0bp to feature; MODIFIER silent_mutation Average:39.49; most accessible tissue: Callus, score: 78.954 N N N N
vg0906798732 A -> G LOC_Os09g12020-LOC_Os09g12050 intergenic_region ; MODIFIER silent_mutation Average:39.49; most accessible tissue: Callus, score: 78.954 N N N N
vg0906798732 A -> DEL N N silent_mutation Average:39.49; most accessible tissue: Callus, score: 78.954 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906798732 NA 8.38E-06 mr1633_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
vg0906798732 3.78E-06 NA mr1646_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