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Detailed information for vg0313128846:

Variant ID: vg0313128846 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 13128846
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


TGTGGGACAAGCCAAGGCTCATTGGACCAAGGTCTTGTGCACCCAAACCAGAGATAAGTTCAGTGAGCTGGTTTCTTAACCCTCTCATGAGCTCCATCAC[A/G]
GCACTATTATGAAGGCAGTCAATTTTCTGCAAAAGCACGTCAAATTATAAGCATGATTGGTTGTTCTACATAAACAAAACAACCAGGAGCCTAACTAACC

Reverse complement sequence

GGTTAGTTAGGCTCCTGGTTGTTTTGTTTATGTAGAACAACCAATCATGCTTATAATTTGACGTGCTTTTGCAGAAAATTGACTGCCTTCATAATAGTGC[T/C]
GTGATGGAGCTCATGAGAGGGTTAAGAAACCAGCTCACTGAACTTATCTCTGGTTTGGGTGCACAAGACCTTGGTCCAATGAGCCTTGGCTTGTCCCACA

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 95.60% 4.30% 0.02% 0.00% NA
All Indica  2759 95.80% 4.20% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 68.00% 32.00% 0.00% 0.00% NA
Indica I  595 92.60% 7.40% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 95.70% 4.30% 0.00% 0.00% NA
Indica Intermediate  786 96.30% 3.60% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0313128846 A -> G LOC_Os03g22730.1 synonymous_variant ; p.Ala109Ala; LOW synonymous_codon Average:45.473; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0313128846 NA 4.21E-06 mr1004 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
vg0313128846 8.32E-07 6.85E-09 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
vg0313128846 NA 2.30E-06 mr1400 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
vg0313128846 NA 4.34E-07 mr1424 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
vg0313128846 NA 6.26E-06 mr1485 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
vg0313128846 NA 4.08E-06 mr1574 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
vg0313128846 NA 5.31E-07 mr1762 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
vg0313128846 1.43E-07 NA mr1916 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