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Detailed information for vg0205720488:

Variant ID: vg0205720488 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5720488
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


AATGCATTGACTGTGGATTTCCCTTAAAGATTTCTGATCAAAATCTGATAGAAGCACAAAGGAATACAAGCAAAGGCCTGTACAAATAAAACTACATGGC[A/G]
CACCAATAAAGGGCCATATAAAAAAAATAGACAGATAGAAGTTATTAAGCATTACCTTGTTTCCATTCATTGCTAAATTGCTACTGCCAGGAGATTGTAA

Reverse complement sequence

TTACAATCTCCTGGCAGTAGCAATTTAGCAATGAATGGAAACAAGGTAATGCTTAATAACTTCTATCTGTCTATTTTTTTTATATGGCCCTTTATTGGTG[T/C]
GCCATGTAGTTTTATTTGTACAGGCCTTTGCTTGTATTCCTTTGTGCTTCTATCAGATTTTGATCAGAAATCTTTAAGGGAAATCCACAGTCAATGCATT

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 70.00% 30.00% 0.06% 0.00% NA
All Indica  2759 96.60% 3.40% 0.07% 0.00% NA
All Japonica  1512 15.10% 84.90% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 99.40% 0.40% 0.22% 0.00% NA
Indica III  913 93.00% 6.90% 0.11% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 0.00% 0.00% NA
Temperate Japonica  767 2.10% 97.90% 0.00% 0.00% NA
Tropical Japonica  504 39.30% 60.70% 0.00% 0.00% NA
Japonica Intermediate  241 6.20% 93.80% 0.00% 0.00% NA
VI/Aromatic  96 84.40% 15.60% 0.00% 0.00% NA
Intermediate  90 71.10% 27.80% 1.11% 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
vg0205720488 A -> G LOC_Os02g10790.1 intron_variant ; MODIFIER silent_mutation Average:46.757; most accessible tissue: Callus, score: 80.065 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205720488 NA 1.11E-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
vg0205720488 NA 4.73E-10 mr1322 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
vg0205720488 NA 9.91E-19 mr1557 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
vg0205720488 NA 3.75E-06 mr1646 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
vg0205720488 4.09E-07 2.16E-21 mr1653 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
vg0205720488 NA 3.55E-17 mr1557_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
vg0205720488 NA 1.56E-29 mr1653_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
vg0205720488 NA 4.60E-11 mr1986_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