Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0113340332:

Variant ID: vg0113340332 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 13340332
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.60, A: 0.40, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:


CACCGACTGGCGGAGGAGAAGGAATCCCGGCTCCGACGGGAGGCTAGAGGAGGAGTCCTTCCTGGCACCTGCGGGCGGAGATGGAGGATTTCTTCCCGGC[A/G]
CCAAGGGATGCGCTCGTCGATCCCGACACTCCAGGCGGCAGCGGCTCGTCATTCCCGGTGCCGGCGGAGTTGAAGTCCAAGCGGCGGCGGCTCGTCATTC

Reverse complement sequence

GAATGACGAGCCGCCGCCGCTTGGACTTCAACTCCGCCGGCACCGGGAATGACGAGCCGCTGCCGCCTGGAGTGTCGGGATCGACGAGCGCATCCCTTGG[T/C]
GCCGGGAAGAAATCCTCCATCTCCGCCCGCAGGTGCCAGGAAGGACTCCTCCTCTAGCCTCCCGTCGGAGCCGGGATTCCTTCTCCTCCGCCAGTCGGTG

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 90.30% 9.70% 0.02% 0.00% NA
All Indica  2759 95.00% 5.00% 0.04% 0.00% NA
All Japonica  1512 81.80% 18.20% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 90.60% 9.40% 0.00% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 97.00% 2.80% 0.11% 0.00% NA
Indica Intermediate  786 95.00% 5.00% 0.00% 0.00% NA
Temperate Japonica  767 95.40% 4.60% 0.00% 0.00% NA
Tropical Japonica  504 58.90% 41.10% 0.00% 0.00% NA
Japonica Intermediate  241 86.30% 13.70% 0.00% 0.00% NA
VI/Aromatic  96 67.70% 32.30% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0113340332 A -> G LOC_Os01g23700.1 synonymous_variant ; p.Gly130Gly; LOW synonymous_codon Average:75.046; most accessible tissue: Zhenshan97 panicle, score: 81.752 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113340332 NA 3.79E-07 mr1543 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
vg0113340332 5.94E-08 1.32E-14 mr1871 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
vg0113340332 NA 2.81E-09 mr1871 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