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Detailed information for vg1217691881:

Variant ID: vg1217691881 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17691881
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


AATAGAAACTTATAGCACTAGCAAATATGAAACTTGGCCATTCGCTGTTTAATTGTAGTTAAATATCTAAATACATTGATTTTAAGCAGCCATATTTAAC[G/A]
CGGTGACAAAAGCGCAACTACAACAGACAAACGGTTCCATTTCTTCTGCTGCTCTTAGTTTGAGCCGAAGCAGCCCTCTTCCTTTTACTATGTCCGATCA

Reverse complement sequence

TGATCGGACATAGTAAAAGGAAGAGGGCTGCTTCGGCTCAAACTAAGAGCAGCAGAAGAAATGGAACCGTTTGTCTGTTGTAGTTGCGCTTTTGTCACCG[C/T]
GTTAAATATGGCTGCTTAAAATCAATGTATTTAGATATTTAACTACAATTAAACAGCGAATGGCCAAGTTTCATATTTGCTAGTGCTATAAGTTTCTATT

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 96.40% 2.70% 0.13% 0.72% NA
All Indica  2759 93.90% 4.60% 0.22% 1.23% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.20% 1.20% 0.17% 0.50% NA
Indica II  465 92.00% 6.00% 0.65% 1.29% NA
Indica III  913 92.60% 6.90% 0.00% 0.55% NA
Indica Intermediate  786 93.40% 3.80% 0.25% 2.54% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1217691881 G -> DEL N N silent_mutation Average:40.011; most accessible tissue: Zhenshan97 young leaf, score: 60.8 N N N N
vg1217691881 G -> A LOC_Os12g29670.1 upstream_gene_variant ; 3162.0bp to feature; MODIFIER silent_mutation Average:40.011; most accessible tissue: Zhenshan97 young leaf, score: 60.8 N N N N
vg1217691881 G -> A LOC_Os12g29660.1 intron_variant ; MODIFIER silent_mutation Average:40.011; most accessible tissue: Zhenshan97 young leaf, score: 60.8 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217691881 NA 1.67E-08 mr1768_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