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Detailed information for vg0912675777:

Variant ID: vg0912675777 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 12675777
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACCTAAAGTTTATAGACCCAAAGTTTATAAGTCAAAAGTTTACATACCCGATTCAAATTTGAATTTGAATACAAATATTAATTTATAGACCCAAAGTTT[A/G]
TAAGTCAAAAATTTACATAACCGTTTCAATTCTGAATTTAAATTTAAATATTTATGATGTAGTAGGAAGAGAAAAAGGGAAGGAGGAAGGGGGGAGAGGA

Reverse complement sequence

TCCTCTCCCCCCTTCCTCCTTCCCTTTTTCTCTTCCTACTACATCATAAATATTTAAATTTAAATTCAGAATTGAAACGGTTATGTAAATTTTTGACTTA[T/C]
AAACTTTGGGTCTATAAATTAATATTTGTATTCAAATTCAAATTTGAATCGGGTATGTAAACTTTTGACTTATAAACTTTGGGTCTATAAACTTTAGGTG

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 96.10% 3.80% 0.08% 0.00% NA
All Indica  2759 93.80% 6.10% 0.14% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 90.30% 9.10% 0.67% 0.00% NA
Indica II  465 95.30% 4.70% 0.00% 0.00% NA
Indica III  913 94.50% 5.50% 0.00% 0.00% NA
Indica Intermediate  786 94.70% 5.30% 0.00% 0.00% NA
Temperate Japonica  767 99.10% 0.90% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0912675777 A -> G LOC_Os09g21020.1 upstream_gene_variant ; 1497.0bp to feature; MODIFIER silent_mutation Average:25.742; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg0912675777 A -> G LOC_Os09g21010.1 downstream_gene_variant ; 3753.0bp to feature; MODIFIER silent_mutation Average:25.742; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg0912675777 A -> G LOC_Os09g21010-LOC_Os09g21020 intergenic_region ; MODIFIER silent_mutation Average:25.742; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0912675777 9.95E-06 6.22E-06 mr1150 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
vg0912675777 6.89E-07 7.89E-06 mr1247_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