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Detailed information for vg0715383438:

Variant ID: vg0715383438 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 15383438
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.07, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


CGATCGACGTAGGCAACGCAGTTGCGCTTGTACTGCTCGATGATGTTGCACTACTAGAAAAATAGTTTTTCGAGGCAGCCAAAAATGGTTTTTCAGGCGG[G/A]
GGAAAGGACCGCCTGCATGCAAAGACTTGCGAAAATAGATGGGTCCACCATTGAAAATCATTTTTGCAGGCGGCATCTATTTTTATAGGCGGTAGAACCA

Reverse complement sequence

TGGTTCTACCGCCTATAAAAATAGATGCCGCCTGCAAAAATGATTTTCAATGGTGGACCCATCTATTTTCGCAAGTCTTTGCATGCAGGCGGTCCTTTCC[C/T]
CCGCCTGAAAAACCATTTTTGGCTGCCTCGAAAAACTATTTTTCTAGTAGTGCAACATCATCGAGCAGTACAAGCGCAACTGCGTTGCCTACGTCGATCG

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 77.90% 22.10% 0.02% 0.00% NA
All Indica  2759 70.30% 29.70% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 23.40% 76.60% 0.00% 0.00% NA
Indica I  595 60.50% 39.50% 0.00% 0.00% NA
Indica II  465 91.20% 8.80% 0.00% 0.00% NA
Indica III  913 69.00% 31.00% 0.00% 0.00% NA
Indica Intermediate  786 66.80% 33.20% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 85.60% 13.30% 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
vg0715383438 G -> A LOC_Os07g26670.1 downstream_gene_variant ; 2438.0bp to feature; MODIFIER silent_mutation Average:75.706; most accessible tissue: Callus, score: 88.1 N N N N
vg0715383438 G -> A LOC_Os07g26660-LOC_Os07g26670 intergenic_region ; MODIFIER silent_mutation Average:75.706; most accessible tissue: Callus, score: 88.1 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715383438 NA 3.26E-06 mr1028 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
vg0715383438 NA 8.29E-06 mr1397 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
vg0715383438 NA 3.62E-08 mr1857 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