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Detailed information for vg0915238489:

Variant ID: vg0915238489 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 15238489
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGTTGCTTTAAAAAATCATATTAATTATTTTTTAAAGTTTTTTTATAGCTAGCACTTAATTAATCACGTGTTAATCTATCGTTCCATTTCTGTGTGAAGG[G/A]
AAGGGGTTCCCAACCCCTAAAAAAACACAGCCTAAAAAGGCTGCTTTGTTCTCAGTTCTCACGCACACCTGCGGACCTACGTTCGCATGATGCAGGGAAA

Reverse complement sequence

TTTCCCTGCATCATGCGAACGTAGGTCCGCAGGTGTGCGTGAGAACTGAGAACAAAGCAGCCTTTTTAGGCTGTGTTTTTTTAGGGGTTGGGAACCCCTT[C/T]
CCTTCACACAGAAATGGAACGATAGATTAACACGTGATTAATTAAGTGCTAGCTATAAAAAAACTTTAAAAAATAATTAATATGATTTTTTAAAGCAACT

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 96.50% 3.30% 0.23% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 89.40% 9.90% 0.66% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 79.80% 18.90% 1.30% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 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
vg0915238489 G -> A LOC_Os09g25420.1 upstream_gene_variant ; 665.0bp to feature; MODIFIER silent_mutation Average:65.258; most accessible tissue: Callus, score: 84.774 N N N N
vg0915238489 G -> A LOC_Os09g25410.1 downstream_gene_variant ; 2485.0bp to feature; MODIFIER silent_mutation Average:65.258; most accessible tissue: Callus, score: 84.774 N N N N
vg0915238489 G -> A LOC_Os09g25430.1 downstream_gene_variant ; 1957.0bp to feature; MODIFIER silent_mutation Average:65.258; most accessible tissue: Callus, score: 84.774 N N N N
vg0915238489 G -> A LOC_Os09g25410.2 downstream_gene_variant ; 2485.0bp to feature; MODIFIER silent_mutation Average:65.258; most accessible tissue: Callus, score: 84.774 N N N N
vg0915238489 G -> A LOC_Os09g25420-LOC_Os09g25430 intergenic_region ; MODIFIER silent_mutation Average:65.258; most accessible tissue: Callus, score: 84.774 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0915238489 NA 3.01E-06 mr1138_2 Jap_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
vg0915238489 NA 2.58E-07 mr1354_2 Jap_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
vg0915238489 3.90E-07 3.90E-07 mr1406_2 Jap_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