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Detailed information for vg1207539306:

Variant ID: vg1207539306 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7539306
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 128. )

Flanking Sequence (100 bp) in Reference Genome:


GGCGGAAACCAAATGACCGGAAGAAAAAAAACCCAAATGGCTCGCCCGCGATCGCCGGGGCGGCTGCTCTCAACCTCGACGGCAAAATAAGAGCCCCCAT[C/A]
TTACACAAGCCTCTCAGTTGAGCCCCAGAAATCATCTGACATTCAGCCACATTATTAAATACCCCCTGAATTCTTATAGTTTCCCCATGTTCTTCATACT

Reverse complement sequence

AGTATGAAGAACATGGGGAAACTATAAGAATTCAGGGGGTATTTAATAATGTGGCTGAATGTCAGATGATTTCTGGGGCTCAACTGAGAGGCTTGTGTAA[G/T]
ATGGGGGCTCTTATTTTGCCGTCGAGGTTGAGAGCAGCCGCCCCGGCGATCGCGGGCGAGCCATTTGGGTTTTTTTTCTTCCGGTCATTTGGTTTCCGCC

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 92.60% 6.10% 1.33% 0.00% NA
All Indica  2759 87.50% 10.30% 2.28% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.80% 0.50% 2.69% 0.00% NA
Indica II  465 58.70% 36.10% 5.16% 0.00% NA
Indica III  913 98.10% 1.80% 0.11% 0.00% NA
Indica Intermediate  786 85.00% 12.20% 2.80% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 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 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg1207539306 C -> A LOC_Os12g13445.1 upstream_gene_variant ; 1285.0bp to feature; MODIFIER silent_mutation Average:60.016; most accessible tissue: Zhenshan97 young leaf, score: 77.736 N N N N
vg1207539306 C -> A LOC_Os12g13440.1 downstream_gene_variant ; 4182.0bp to feature; MODIFIER silent_mutation Average:60.016; most accessible tissue: Zhenshan97 young leaf, score: 77.736 N N N N
vg1207539306 C -> A LOC_Os12g13450.1 downstream_gene_variant ; 191.0bp to feature; MODIFIER silent_mutation Average:60.016; most accessible tissue: Zhenshan97 young leaf, score: 77.736 N N N N
vg1207539306 C -> A LOC_Os12g13440.2 downstream_gene_variant ; 4212.0bp to feature; MODIFIER silent_mutation Average:60.016; most accessible tissue: Zhenshan97 young leaf, score: 77.736 N N N N
vg1207539306 C -> A LOC_Os12g13445-LOC_Os12g13450 intergenic_region ; MODIFIER silent_mutation Average:60.016; most accessible tissue: Zhenshan97 young leaf, score: 77.736 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207539306 5.46E-07 9.12E-11 mr1024_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
vg1207539306 NA 3.62E-13 mr1565_2 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
vg1207539306 NA 6.10E-11 mr1565_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