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Detailed information for vg1005268365:

Variant ID: vg1005268365 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5268365
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.55, A: 0.41, T: 0.03, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:


ACAAACAAAAAAAATTATCATAATATAATCATGTAAGATCTTGTTGTATAGATTTAATTGTAGGGAACACAACGGTATAATTGGATCATAGATCAGATAA[A/G]
TAATTTAAGAGAATATTTTATTTGAAATAATGAGGATGCAAGTGGCAGGTGCTAGGCATTCATTAAAGTCACTTTCTTTTTTTATAAGTTACTTCTATAA

Reverse complement sequence

TTATAGAAGTAACTTATAAAAAAAGAAAGTGACTTTAATGAATGCCTAGCACCTGCCACTTGCATCCTCATTATTTCAAATAAAATATTCTCTTAAATTA[T/C]
TTATCTGATCTATGATCCAATTATACCGTTGTGTTCCCTACAATTAAATCTATACAACAAGATCTTACATGATTATATTATGATAATTTTTTTTGTTTGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.20% 41.60% 0.17% 4.10% NA
All Indica  2759 41.50% 58.10% 0.14% 0.33% NA
All Japonica  1512 86.20% 3.40% 0.26% 10.12% NA
Aus  269 3.30% 96.30% 0.00% 0.37% NA
Indica I  595 21.30% 78.50% 0.17% 0.00% NA
Indica II  465 51.20% 48.80% 0.00% 0.00% NA
Indica III  913 53.20% 46.00% 0.22% 0.55% NA
Indica Intermediate  786 37.30% 62.10% 0.13% 0.51% NA
Temperate Japonica  767 78.60% 3.50% 0.52% 17.34% NA
Tropical Japonica  504 97.00% 2.20% 0.00% 0.79% NA
Japonica Intermediate  241 87.60% 5.80% 0.00% 6.64% NA
VI/Aromatic  96 47.90% 27.10% 0.00% 25.00% NA
Intermediate  90 64.40% 27.80% 0.00% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1005268365 A -> G LOC_Os10g09740.1 downstream_gene_variant ; 758.0bp to feature; MODIFIER silent_mutation Average:19.101; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg1005268365 A -> G LOC_Os10g09710-LOC_Os10g09740 intergenic_region ; MODIFIER silent_mutation Average:19.101; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg1005268365 A -> DEL N N silent_mutation Average:19.101; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005268365 NA 7.10E-09 mr1050 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
vg1005268365 NA 1.45E-07 mr1222 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
vg1005268365 NA 5.75E-07 mr1245 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
vg1005268365 NA 7.84E-06 mr1308 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
vg1005268365 NA 5.65E-07 mr1420 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
vg1005268365 NA 2.83E-06 mr1445 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
vg1005268365 NA 7.07E-06 mr1681 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
vg1005268365 NA 1.23E-09 mr1730 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
vg1005268365 NA 5.12E-07 mr1764 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
vg1005268365 NA 1.27E-07 mr1779 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
vg1005268365 NA 2.09E-07 mr1810 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
vg1005268365 NA 8.49E-06 mr1832 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
vg1005268365 NA 2.72E-10 mr1866 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
vg1005268365 NA 8.52E-09 mr1986 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
vg1005268365 7.46E-07 7.46E-07 mr1281_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