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Detailed information for vg1207394291:

Variant ID: vg1207394291 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7394291
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, C: 0.02, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


TTGCTTACATTTGTAATAGTTTTAGTAATTTTGGAATGAACGTGCAGCTTGGAATGTATAATGTTTTTTGGTTTGAAATGCCAAATATATATGTATATTG[G/C]
TTTATTAAAAAAACTTCAATTCCATTTGCACACTCTAGATATTTGCGACGCTTCAGTTATGTATAATTTTAGCCTTGCGCGAATCTTTTTGATAGATTGC

Reverse complement sequence

GCAATCTATCAAAAAGATTCGCGCAAGGCTAAAATTATACATAACTGAAGCGTCGCAAATATCTAGAGTGTGCAAATGGAATTGAAGTTTTTTTAATAAA[C/G]
CAATATACATATATATTTGGCATTTCAAACCAAAAAACATTATACATTCCAAGCTGCACGTTCATTCCAAAATTACTAAAACTATTACAAATGTAAGCAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.90% 12.00% 0.08% 0.00% NA
All Indica  2759 87.40% 12.60% 0.07% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 45.00% 54.30% 0.74% 0.00% NA
Indica I  595 89.20% 10.80% 0.00% 0.00% NA
Indica II  465 91.00% 9.00% 0.00% 0.00% NA
Indica III  913 88.20% 11.80% 0.00% 0.00% NA
Indica Intermediate  786 82.80% 16.90% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 34.40% 65.60% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg1207394291 G -> C LOC_Os12g13290.1 downstream_gene_variant ; 440.0bp to feature; MODIFIER silent_mutation Average:18.891; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N
vg1207394291 G -> C LOC_Os12g13290-LOC_Os12g13295 intergenic_region ; MODIFIER silent_mutation Average:18.891; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207394291 4.06E-06 NA mr1032 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
vg1207394291 5.45E-06 NA mr1165 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
vg1207394291 3.02E-06 1.98E-06 mr1590 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
vg1207394291 NA 1.44E-06 mr1808 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
vg1207394291 NA 6.51E-08 mr1815 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