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Detailed information for vg0619510251:

Variant ID: vg0619510251 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 19510251
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


GACAACAGATTGAAAACCATTCATCAACTTAATCAAGATGAAATATGATTTGTTTTTGGTTGGCATTTTAGATCAACACTATTACTTTAAAAAAATATAT[G/A]
TTGTATATAGGATATACACTTACACAGGTGCTAACAACTAAAAGTTTATATCCATATGTAATCTTATATAACTCTAATTACAATACATATTTATTATCCT

Reverse complement sequence

AGGATAATAAATATGTATTGTAATTAGAGTTATATAAGATTACATATGGATATAAACTTTTAGTTGTTAGCACCTGTGTAAGTGTATATCCTATATACAA[C/T]
ATATATTTTTTTAAAGTAATAGTGTTGATCTAAAATGCCAACCAAAAACAAATCATATTTCATCTTGATTAAGTTGATGAATGGTTTTCAATCTGTTGTC

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 87.80% 10.50% 1.71% 0.00% NA
All Indica  2759 79.50% 17.70% 2.83% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 89.10% 5.20% 5.71% 0.00% NA
Indica II  465 86.20% 10.80% 3.01% 0.00% NA
Indica III  913 65.30% 33.70% 0.99% 0.00% NA
Indica Intermediate  786 84.90% 12.50% 2.67% 0.00% NA
Temperate Japonica  767 99.30% 0.50% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 91.10% 6.70% 2.22% 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
vg0619510251 G -> A LOC_Os06g33480.1 upstream_gene_variant ; 3835.0bp to feature; MODIFIER silent_mutation Average:35.878; most accessible tissue: Callus, score: 65.948 N N N N
vg0619510251 G -> A LOC_Os06g33510.1 upstream_gene_variant ; 3393.0bp to feature; MODIFIER silent_mutation Average:35.878; most accessible tissue: Callus, score: 65.948 N N N N
vg0619510251 G -> A LOC_Os06g33490.1 intron_variant ; MODIFIER silent_mutation Average:35.878; most accessible tissue: Callus, score: 65.948 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0619510251 NA 7.12E-10 mr1695 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
vg0619510251 2.52E-07 NA mr1087_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
vg0619510251 1.42E-10 NA mr1695_2 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
vg0619510251 6.88E-08 1.12E-11 mr1695_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