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Detailed information for vg0308773264:

Variant ID: vg0308773264 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 8773264
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGAAACGATTAAATAGGGAAGAACGAGACGGCGTGGGAGAGGAGACAAAAAAAAAAGGGATGGGACTCAGGAATGGCATGGTTTCAATTTTAGAAATTTC[C/T]
AGTGAACATGTAGCCGATATGACGAATAGTAGTGATATTTTTTTAATTTCGCAAAGTTGTAGTGCATTGATCCAATTAACTCTTTGTTTTTAGCATTTGA

Reverse complement sequence

TCAAATGCTAAAAACAAAGAGTTAATTGGATCAATGCACTACAACTTTGCGAAATTAAAAAAATATCACTACTATTCGTCATATCGGCTACATGTTCACT[G/A]
GAAATTTCTAAAATTGAAACCATGCCATTCCTGAGTCCCATCCCTTTTTTTTTTGTCTCCTCTCCCACGCCGTCTCGTTCTTCCCTATTTAATCGTTTCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.90% 1.10% 0.04% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.60% 3.30% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 96.50% 3.30% 0.26% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 90.90% 9.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0308773264 C -> T LOC_Os03g15890.1 upstream_gene_variant ; 2716.0bp to feature; MODIFIER silent_mutation Average:41.888; most accessible tissue: Callus, score: 54.925 N N N N
vg0308773264 C -> T LOC_Os03g15900.2 upstream_gene_variant ; 2919.0bp to feature; MODIFIER silent_mutation Average:41.888; most accessible tissue: Callus, score: 54.925 N N N N
vg0308773264 C -> T LOC_Os03g15890.3 upstream_gene_variant ; 2754.0bp to feature; MODIFIER silent_mutation Average:41.888; most accessible tissue: Callus, score: 54.925 N N N N
vg0308773264 C -> T LOC_Os03g15890.2 upstream_gene_variant ; 2728.0bp to feature; MODIFIER silent_mutation Average:41.888; most accessible tissue: Callus, score: 54.925 N N N N
vg0308773264 C -> T LOC_Os03g15890-LOC_Os03g15900 intergenic_region ; MODIFIER silent_mutation Average:41.888; most accessible tissue: Callus, score: 54.925 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0308773264 NA 1.16E-07 mr1565_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
vg0308773264 4.93E-06 4.93E-06 mr1940_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