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Detailed information for vg0219293036:

Variant ID: vg0219293036 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 19293036
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


AGCTAGAGCTGGAGCTGTGCTAAACATGCCCCCAGTCAGTTAAGCTACGCTCACTTCACATTTGAAATTGCTTTTGAAACAACCTCATTTCACTTTTCCA[G/T]
GACGGTAAAAAAAATAGCATCTTTTGTGCTACTTAAGGATTATTATTTATCCGGAACACAGAAATGCTATAAGTTTCCATAGAAGTTAATTTAAACCATA

Reverse complement sequence

TATGGTTTAAATTAACTTCTATGGAAACTTATAGCATTTCTGTGTTCCGGATAAATAATAATCCTTAAGTAGCACAAAAGATGCTATTTTTTTTACCGTC[C/A]
TGGAAAAGTGAAATGAGGTTGTTTCAAAAGCAATTTCAAATGTGAAGTGAGCGTAGCTTAACTGACTGGGGGCATGTTTAGCACAGCTCCAGCTCTAGCT

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 98.30% 1.30% 0.42% 0.00% NA
All Indica  2759 99.90% 0.00% 0.11% 0.00% NA
All Japonica  1512 94.80% 4.10% 1.12% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.50% 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 90.20% 8.00% 1.83% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 0.40% 1.24% 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
vg0219293036 G -> T LOC_Os02g32570.1 upstream_gene_variant ; 1435.0bp to feature; MODIFIER silent_mutation Average:59.504; most accessible tissue: Zhenshan97 panicle, score: 75.67 N N N N
vg0219293036 G -> T LOC_Os02g32570.2 upstream_gene_variant ; 3128.0bp to feature; MODIFIER silent_mutation Average:59.504; most accessible tissue: Zhenshan97 panicle, score: 75.67 N N N N
vg0219293036 G -> T LOC_Os02g32560-LOC_Os02g32570 intergenic_region ; MODIFIER silent_mutation Average:59.504; most accessible tissue: Zhenshan97 panicle, score: 75.67 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0219293036 NA 2.20E-07 mr1062 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
vg0219293036 NA 3.25E-07 mr1210 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
vg0219293036 NA 8.29E-07 mr1305 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
vg0219293036 NA 2.69E-08 mr1515 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
vg0219293036 NA 8.32E-10 mr1585 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
vg0219293036 NA 6.47E-08 mr1586 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
vg0219293036 NA 1.63E-06 mr1765 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
vg0219293036 NA 4.68E-07 mr1305_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
vg0219293036 1.86E-06 1.86E-06 mr1317_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
vg0219293036 NA 9.36E-08 mr1585_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
vg0219293036 3.23E-06 3.23E-06 mr1927_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