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Detailed information for vg1127982448:

Variant ID: vg1127982448 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27982448
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, G: 0.08, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


ATAACTTCTACAAAACCAAATTAATTGCCCCAAAAATCTCACTATTAATTTGTTTTAATACGTAGAAAATAACGGGTATTTGGCTAGTATAGTAGTATGT[G/A]
CCAATTGTGTAGCTGAATTGGTAGCTTGTGTAGCTTAATTATAAGCAATTGTAAAAAAAAATGAGCAAATTGTGTAGCTGAATTATACATTGTAAAAAAA

Reverse complement sequence

TTTTTTTACAATGTATAATTCAGCTACACAATTTGCTCATTTTTTTTTACAATTGCTTATAATTAAGCTACACAAGCTACCAATTCAGCTACACAATTGG[C/T]
ACATACTACTATACTAGCCAAATACCCGTTATTTTCTACGTATTAAAACAAATTAATAGTGAGATTTTTGGGGCAATTAATTTGGTTTTGTAGAAGTTAT

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 40.80% 15.10% 1.90% 42.21% NA
All Indica  2759 56.80% 4.70% 1.30% 37.15% NA
All Japonica  1512 15.40% 29.10% 1.98% 53.51% NA
Aus  269 28.30% 42.40% 7.06% 22.30% NA
Indica I  595 50.30% 7.20% 1.18% 41.34% NA
Indica II  465 40.40% 7.10% 1.29% 51.18% NA
Indica III  913 71.30% 0.20% 0.22% 28.26% NA
Indica Intermediate  786 54.60% 6.70% 2.67% 36.01% NA
Temperate Japonica  767 12.10% 22.30% 0.78% 64.80% NA
Tropical Japonica  504 22.40% 36.10% 2.18% 39.29% NA
Japonica Intermediate  241 11.20% 36.10% 5.39% 47.30% NA
VI/Aromatic  96 17.70% 8.30% 3.12% 70.83% NA
Intermediate  90 36.70% 24.40% 2.22% 36.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127982448 G -> A LOC_Os11g46210.1 upstream_gene_variant ; 2249.0bp to feature; MODIFIER silent_mutation Average:21.605; most accessible tissue: Callus, score: 81.564 N N N N
vg1127982448 G -> A LOC_Os11g46200.1 intron_variant ; MODIFIER silent_mutation Average:21.605; most accessible tissue: Callus, score: 81.564 N N N N
vg1127982448 G -> DEL N N silent_mutation Average:21.605; most accessible tissue: Callus, score: 81.564 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127982448 NA 5.30E-06 mr1345 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
vg1127982448 1.25E-07 1.25E-07 mr1459 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
vg1127982448 6.67E-07 NA mr1745 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
vg1127982448 NA 5.28E-06 mr1759 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