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Detailed information for vg0915182972:

Variant ID: vg0915182972 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 15182972
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTAGAAATTCTAACATCAATCAGAGAAAAAAAATAAGAGTTCAAGTAGAAATGCAATTTAGAAATAACTGAAATTCAGAATATTGAAATAACAATCCATC[C/A]
AGAATACCAAATGATAATTAATTAAGATTTGAATTAAAAAATAATAATTTCCAAAATGAAAAAATAAAAAAAAGATTTTTAGTAGGGATACAATATAAAA

Reverse complement sequence

TTTTATATTGTATCCCTACTAAAAATCTTTTTTTTATTTTTTCATTTTGGAAATTATTATTTTTTAATTCAAATCTTAATTAATTATCATTTGGTATTCT[G/T]
GATGGATTGTTATTTCAATATTCTGAATTTCAGTTATTTCTAAATTGCATTTCTACTTGAACTCTTATTTTTTTTCTCTGATTGATGTTAGAATTTCTAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.30% 4.70% 4.97% 0.00% NA
All Indica  2759 83.50% 8.10% 8.37% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 84.50% 0.70% 14.79% 0.00% NA
Indica II  465 86.00% 4.30% 9.68% 0.00% NA
Indica III  913 82.90% 13.80% 3.29% 0.00% NA
Indica Intermediate  786 81.90% 9.40% 8.65% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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% 0.00% 4.44% 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
vg0915182972 C -> A LOC_Os09g25340.1 upstream_gene_variant ; 3167.0bp to feature; MODIFIER silent_mutation Average:23.059; most accessible tissue: Callus, score: 41.973 N N N N
vg0915182972 C -> A LOC_Os09g25330-LOC_Os09g25340 intergenic_region ; MODIFIER silent_mutation Average:23.059; most accessible tissue: Callus, score: 41.973 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0915182972 2.41E-06 6.40E-07 mr1006_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