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Detailed information for vg0713247684:

Variant ID: vg0713247684 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 13247684
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


GGTGGCGGAAAGACCGGCTGCTCGGTCGAAACTTTCCGTAGGCGTCTACGGAGGCACGCAGCACACGAGCGAAGGGGAAGACGAGCCATCGCGGAAGAAC[A/C]
GGGAGCAGTCGCGCAAAGCGCTTCCCAAAAACCTTATTGCCGCCTTCTCCCGGTGCAGGACGTCGAAGGCAGAGGTTCCAGAGACCTGCTCTCCCGATCG

Reverse complement sequence

CGATCGGGAGAGCAGGTCTCTGGAACCTCTGCCTTCGACGTCCTGCACCGGGAGAAGGCGGCAATAAGGTTTTTGGGAAGCGCTTTGCGCGACTGCTCCC[T/G]
GTTCTTCCGCGATGGCTCGTCTTCCCCTTCGCTCGTGTGCTGCGTGCCTCCGTAGACGCCTACGGAAAGTTTCGACCGAGCAGCCGGTCTTTCCGCCACC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.60% 3.30% 1.10% 0.00% NA
All Indica  2759 92.60% 5.50% 1.85% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 74.10% 19.70% 6.22% 0.00% NA
Indica II  465 98.30% 0.60% 1.08% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 94.70% 4.20% 1.15% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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 97.80% 1.10% 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
vg0713247684 A -> C LOC_Os07g23450.1 downstream_gene_variant ; 793.0bp to feature; MODIFIER silent_mutation Average:46.033; most accessible tissue: Minghui63 flag leaf, score: 61.847 N N N N
vg0713247684 A -> C LOC_Os07g23460.1 downstream_gene_variant ; 990.0bp to feature; MODIFIER silent_mutation Average:46.033; most accessible tissue: Minghui63 flag leaf, score: 61.847 N N N N
vg0713247684 A -> C LOC_Os07g23450-LOC_Os07g23460 intergenic_region ; MODIFIER silent_mutation Average:46.033; most accessible tissue: Minghui63 flag leaf, score: 61.847 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0713247684 NA 1.17E-10 Heading_date Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0713247684 1.35E-06 NA mr1378_2 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
vg0713247684 2.88E-07 7.50E-07 mr1378_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