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Detailed information for vg0715234696:

Variant ID: vg0715234696 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 15234696
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, C: 0.04, others allele: 0.00, population size: 57. )

Flanking Sequence (100 bp) in Reference Genome:


GTAAAAAGAAGAAGCCGACGATGACCCCTTCTAGCACCATGGTTCTCGGTTGGCTAAAGCTGAAACATGGTTGGATCTTGGATGAAGCTGAATATCGATG[G/C]
CTCCTTTGCAAAACAAGATGGGGTGGGAATCGGCATGGTCCTTCGAGATTGCCATGGCTCCCCAATTTTTTCAGCATGTCAATTCATCAATTTTTGTAGT

Reverse complement sequence

ACTACAAAAATTGATGAATTGACATGCTGAAAAAATTGGGGAGCCATGGCAATCTCGAAGGACCATGCCGATTCCCACCCCATCTTGTTTTGCAAAGGAG[C/G]
CATCGATATTCAGCTTCATCCAAGATCCAACCATGTTTCAGCTTTAGCCAACCGAGAACCATGGTGCTAGAAGGGGTCATCGTCGGCTTCTTCTTTTTAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.70% 35.20% 0.08% 0.00% NA
All Indica  2759 44.00% 55.80% 0.14% 0.00% NA
All Japonica  1512 99.20% 0.80% 0.00% 0.00% NA
Aus  269 75.50% 24.50% 0.00% 0.00% NA
Indica I  595 54.10% 45.50% 0.34% 0.00% NA
Indica II  465 20.90% 78.70% 0.43% 0.00% NA
Indica III  913 43.20% 56.80% 0.00% 0.00% NA
Indica Intermediate  786 51.10% 48.90% 0.00% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 63.30% 36.70% 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
vg0715234696 G -> C LOC_Os07g26480.1 downstream_gene_variant ; 1413.0bp to feature; MODIFIER silent_mutation Average:64.365; most accessible tissue: Minghui63 flag leaf, score: 81.312 N N N N
vg0715234696 G -> C LOC_Os07g26490.1 downstream_gene_variant ; 2470.0bp to feature; MODIFIER silent_mutation Average:64.365; most accessible tissue: Minghui63 flag leaf, score: 81.312 N N N N
vg0715234696 G -> C LOC_Os07g26480.2 downstream_gene_variant ; 1413.0bp to feature; MODIFIER silent_mutation Average:64.365; most accessible tissue: Minghui63 flag leaf, score: 81.312 N N N N
vg0715234696 G -> C LOC_Os07g26490.2 downstream_gene_variant ; 2470.0bp to feature; MODIFIER silent_mutation Average:64.365; most accessible tissue: Minghui63 flag leaf, score: 81.312 N N N N
vg0715234696 G -> C LOC_Os07g26480-LOC_Os07g26490 intergenic_region ; MODIFIER silent_mutation Average:64.365; most accessible tissue: Minghui63 flag leaf, score: 81.312 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715234696 NA 1.15E-06 mr1212 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
vg0715234696 NA 1.46E-06 mr1528 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