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Detailed information for vg0525136576:

Variant ID: vg0525136576 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 25136576
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.20, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


TTTATATGGAGCAACCTGAAGGTTTTGTTGTTCCTGGAAAAGAGAACCTAGTATATAGGTTAAAGAAATCTCTTTATGGGTTAAAGCAGTCACCTAGACA[G/A]
TGGTATAAGAGATTTGACTCTTTCATGTTTTCTCAGAAGTTTAGAAGATCCAATTATGATAGCTGTGTTTATCTTAAAGTTGTTGATGGTTCATCTATAT

Reverse complement sequence

ATATAGATGAACCATCAACAACTTTAAGATAAACACAGCTATCATAATTGGATCTTCTAAACTTCTGAGAAAACATGAAAGAGTCAAATCTCTTATACCA[C/T]
TGTCTAGGTGACTGCTTTAACCCATAAAGAGATTTCTTTAACCTATATACTAGGTTCTCTTTTCCAGGAACAACAAAACCTTCAGGTTGCTCCATATAAA

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 60.00% 39.70% 0.32% 0.00% NA
All Indica  2759 91.30% 8.20% 0.47% 0.00% NA
All Japonica  1512 0.30% 99.70% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 96.50% 2.70% 0.84% 0.00% NA
Indica II  465 76.30% 23.00% 0.65% 0.00% NA
Indica III  913 96.40% 3.20% 0.44% 0.00% NA
Indica Intermediate  786 90.50% 9.40% 0.13% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 0.40% 99.60% 0.00% 0.00% NA
Japonica Intermediate  241 0.00% 100.00% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 40.00% 57.80% 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
vg0525136576 G -> A LOC_Os05g43220.1 synonymous_variant ; p.Gln854Gln; LOW synonymous_codon Average:17.263; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0525136576 NA 2.22E-34 mr1105 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
vg0525136576 8.94E-07 8.95E-07 mr1105 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
vg0525136576 NA 2.26E-09 mr1198 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
vg0525136576 NA 1.19E-08 mr1275 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
vg0525136576 NA 1.42E-26 mr1903 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
vg0525136576 NA 1.28E-08 mr1934 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
vg0525136576 NA 3.40E-08 mr1645_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
vg0525136576 NA 2.48E-09 mr1907_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