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Detailed information for vg1217896758:

Variant ID: vg1217896758 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17896758
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.87, A: 0.13, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


TACCAAAACAGTGGAGAAAACGAGAAAACCTTAACTCTGACTCACTACTATACCTAGGTTGTGTTTAGTTCACACTAAAATTAAAAGTTTGGTTGAAATT[G/A]
GAACGATGTGACGAAAAAGTTGGAAGATTGTGTGTAAGAAAGTTTTGATGTGATGAAAAAGTTGGAAGTTTGAATAATTATTTTGAAACTAAACACGGCC

Reverse complement sequence

GGCCGTGTTTAGTTTCAAAATAATTATTCAAACTTCCAACTTTTTCATCACATCAAAACTTTCTTACACACAATCTTCCAACTTTTTCGTCACATCGTTC[C/T]
AATTTCAACCAAACTTTTAATTTTAGTGTGAACTAAACACAACCTAGGTATAGTAGTGAGTCAGAGTTAAGGTTTTCTCGTTTTCTCCACTGTTTTGGTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 71.90% 28.00% 0.04% 0.00% NA
All Indica  2759 67.50% 32.50% 0.04% 0.00% NA
All Japonica  1512 81.10% 18.90% 0.00% 0.00% NA
Aus  269 65.40% 34.60% 0.00% 0.00% NA
Indica I  595 30.40% 69.60% 0.00% 0.00% NA
Indica II  465 83.40% 16.60% 0.00% 0.00% NA
Indica III  913 78.20% 21.80% 0.00% 0.00% NA
Indica Intermediate  786 73.50% 26.30% 0.13% 0.00% NA
Temperate Japonica  767 97.80% 2.20% 0.00% 0.00% NA
Tropical Japonica  504 64.10% 35.90% 0.00% 0.00% NA
Japonica Intermediate  241 63.50% 36.50% 0.00% 0.00% NA
VI/Aromatic  96 78.10% 21.90% 0.00% 0.00% NA
Intermediate  90 68.90% 30.00% 1.11% 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
vg1217896758 G -> A LOC_Os12g29950.1 upstream_gene_variant ; 4172.0bp to feature; MODIFIER silent_mutation Average:58.282; most accessible tissue: Zhenshan97 panicle, score: 83.904 N N N N
vg1217896758 G -> A LOC_Os12g29950.2 upstream_gene_variant ; 4172.0bp to feature; MODIFIER silent_mutation Average:58.282; most accessible tissue: Zhenshan97 panicle, score: 83.904 N N N N
vg1217896758 G -> A LOC_Os12g29940.1 downstream_gene_variant ; 2201.0bp to feature; MODIFIER silent_mutation Average:58.282; most accessible tissue: Zhenshan97 panicle, score: 83.904 N N N N
vg1217896758 G -> A LOC_Os12g29940-LOC_Os12g29950 intergenic_region ; MODIFIER silent_mutation Average:58.282; most accessible tissue: Zhenshan97 panicle, score: 83.904 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217896758 4.16E-06 NA mr1513 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
vg1217896758 2.61E-06 NA mr1590 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
vg1217896758 NA 7.65E-07 mr1904 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
vg1217896758 NA 5.85E-06 mr1662_2 Jap_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