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Detailed information for vg0336102786:

Variant ID: vg0336102786 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 36102786
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


GGCATATTACCAAAATCCCACGGTCGAATATCCGATTTCTTATGTGGGTCATTCAAGAAAGGGCTATTTGGAAGAAAAGATGTACCATCACCCGATACAT[G/T]
TATCATCATGTTCCATTCAAATGGCTTATCTATTATTTTTAACTTGAAGACTCTATCGTGAGTTTGGGAGCCTATCTGTCGGCTTCTTTTTGTTCTATAT

Reverse complement sequence

ATATAGAACAAAAAGAAGCCGACAGATAGGCTCCCAAACTCACGATAGAGTCTTCAAGTTAAAAATAATAGATAAGCCATTTGAATGGAACATGATGATA[C/A]
ATGTATCGGGTGATGGTACATCTTTTCTTCCAAATAGCCCTTTCTTGAATGACCCACATAAGAAATCGGATATTCGACCGTGGGATTTTGGTAATATGCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.00% 11.00% 0.02% 0.00% NA
All Indica  2759 81.60% 18.30% 0.04% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.30% 3.70% 0.00% 0.00% NA
Indica II  465 88.20% 11.80% 0.00% 0.00% NA
Indica III  913 69.40% 30.60% 0.00% 0.00% NA
Indica Intermediate  786 80.80% 19.10% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 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 87.80% 12.20% 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
vg0336102786 G -> T LOC_Os03g63880.1 upstream_gene_variant ; 4536.0bp to feature; MODIFIER silent_mutation Average:59.069; most accessible tissue: Callus, score: 85.635 N N N N
vg0336102786 G -> T LOC_Os03g63900.1 upstream_gene_variant ; 727.0bp to feature; MODIFIER silent_mutation Average:59.069; most accessible tissue: Callus, score: 85.635 N N N N
vg0336102786 G -> T LOC_Os03g63910.1 upstream_gene_variant ; 4465.0bp to feature; MODIFIER silent_mutation Average:59.069; most accessible tissue: Callus, score: 85.635 N N N N
vg0336102786 G -> T LOC_Os03g63890.1 downstream_gene_variant ; 1905.0bp to feature; MODIFIER silent_mutation Average:59.069; most accessible tissue: Callus, score: 85.635 N N N N
vg0336102786 G -> T LOC_Os03g63890-LOC_Os03g63900 intergenic_region ; MODIFIER silent_mutation Average:59.069; most accessible tissue: Callus, score: 85.635 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0336102786 NA 4.38E-06 mr1291 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
vg0336102786 1.23E-08 2.16E-09 mr1892 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
vg0336102786 4.77E-09 6.81E-09 mr1892 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
vg0336102786 NA 6.02E-06 mr1705_2 Ind_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