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Detailed information for vg0824869424:

Variant ID: vg0824869424 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 24869424
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

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:


CTAACTGATTGAAGATTGGATAATTTATGCCTTTTCTGCCCATATACTAACTGATTGCCTTGTACTTCCACCAATCACAATTATGATGCTTTCTTTAATT[G/A]
TTTGGTGAAGTAGAGTAATAATTAATGCATTTTAATCTCTATGTCTGCAGGTTGTTTCACTAATTTGAATGTAAGCAGTAAGACAGATCATGGTATGTTT

Reverse complement sequence

AAACATACCATGATCTGTCTTACTGCTTACATTCAAATTAGTGAAACAACCTGCAGACATAGAGATTAAAATGCATTAATTATTACTCTACTTCACCAAA[C/T]
AATTAAAGAAAGCATCATAATTGTGATTGGTGGAAGTACAAGGCAATCAGTTAGTATATGGGCAGAAAAGGCATAAATTATCCAATCTTCAATCAGTTAG

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 88.80% 10.80% 0.34% 0.02% NA
All Indica  2759 99.20% 0.80% 0.00% 0.00% NA
All Japonica  1512 73.80% 25.10% 1.06% 0.07% NA
Aus  269 92.90% 7.10% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 1.40% 0.00% 0.00% NA
Temperate Japonica  767 92.20% 5.70% 1.96% 0.13% NA
Tropical Japonica  504 43.80% 56.20% 0.00% 0.00% NA
Japonica Intermediate  241 78.00% 21.60% 0.41% 0.00% NA
VI/Aromatic  96 19.80% 80.20% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0824869424 G -> A LOC_Os08g39350.1 intron_variant ; MODIFIER silent_mutation Average:57.216; most accessible tissue: Zhenshan97 flower, score: 82.359 N N N N
vg0824869424 G -> DEL N N silent_mutation Average:57.216; most accessible tissue: Zhenshan97 flower, score: 82.359 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0824869424 NA 2.82E-07 mr1554 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
vg0824869424 2.08E-06 2.07E-06 mr1601 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
vg0824869424 NA 8.32E-07 mr1602 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
vg0824869424 NA 8.84E-06 mr1602 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
vg0824869424 NA 1.43E-07 mr1916 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
vg0824869424 NA 6.44E-06 mr1295_2 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
vg0824869424 NA 1.50E-07 mr1554_2 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