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Detailed information for vg1214204528:

Variant ID: vg1214204528 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 14204528
Reference Allele: GAlternative Allele: A,C
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: 113. )

Flanking Sequence (100 bp) in Reference Genome:


CGGACACTCAAGACGTAAGTATGATTGAAGCTGACTGGAGAGAGCCCCTCATAAGATTTTTGACCAAACAAGAACTCATCTAAGATAAAGATGAAGCCGA[G/A,C]
TGGATCTCCAGGCGCAGCAGGCTCTATATCATTCATGAGACTGAGCTGTACAAGAAAAGTCCATCAGGAATCCTGCAACGCTGTGTATCTTTGGAGGAGG

Reverse complement sequence

CCTCCTCCAAAGATACACAGCGTTGCAGGATTCCTGATGGACTTTTCTTGTACAGCTCAGTCTCATGAATGATATAGAGCCTGCTGCGCCTGGAGATCCA[C/T,G]
TCGGCTTCATCTTTATCTTAGATGAGTTCTTGTTTGGTCAAAAATCTTATGAGGGGCTCTCTCCAGTCAGCTTCAATCATACTTACGTCTTGAGTGTCCG

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 75.80% 23.70% 0.36% 0.13% C: 0.02%
All Indica  2759 59.70% 39.40% 0.62% 0.22% C: 0.04%
All Japonica  1512 99.40% 0.60% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 45.40% 54.30% 0.34% 0.00% NA
Indica II  465 76.80% 20.20% 2.15% 0.86% NA
Indica III  913 55.50% 44.20% 0.11% 0.00% C: 0.11%
Indica Intermediate  786 65.30% 34.00% 0.51% 0.25% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 84.40% 15.60% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg1214204528 G -> C LOC_Os12g24750.1 downstream_gene_variant ; 1962.0bp to feature; MODIFIER silent_mutation Average:36.921; most accessible tissue: Minghui63 flag leaf, score: 57.188 N N N N
vg1214204528 G -> C LOC_Os12g24770.1 downstream_gene_variant ; 1513.0bp to feature; MODIFIER silent_mutation Average:36.921; most accessible tissue: Minghui63 flag leaf, score: 57.188 N N N N
vg1214204528 G -> C LOC_Os12g24760.1 intron_variant ; MODIFIER silent_mutation Average:36.921; most accessible tissue: Minghui63 flag leaf, score: 57.188 N N N N
vg1214204528 G -> DEL N N silent_mutation Average:36.921; most accessible tissue: Minghui63 flag leaf, score: 57.188 N N N N
vg1214204528 G -> A LOC_Os12g24750.1 downstream_gene_variant ; 1962.0bp to feature; MODIFIER silent_mutation Average:36.921; most accessible tissue: Minghui63 flag leaf, score: 57.188 N N N N
vg1214204528 G -> A LOC_Os12g24770.1 downstream_gene_variant ; 1513.0bp to feature; MODIFIER silent_mutation Average:36.921; most accessible tissue: Minghui63 flag leaf, score: 57.188 N N N N
vg1214204528 G -> A LOC_Os12g24760.1 intron_variant ; MODIFIER silent_mutation Average:36.921; most accessible tissue: Minghui63 flag leaf, score: 57.188 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1214204528 NA 5.45E-08 mr1308 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
vg1214204528 NA 8.72E-06 mr1308_2 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
vg1214204528 NA 4.15E-07 mr1361_2 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