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Detailed information for vg1106988724:

Variant ID: vg1106988724 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 6988724
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TAACAACAACCTCTCCCCCTCAAAACACAAGATCACACATCCCAATGGGGCTCTGCCCCATGACACCCAGAATGCACTTCAGCGGTACATGTTCGACTCT[G/A]
TGTTTTGAACAACGTTTGTAAAAACTACAGAAAAACACCCCCCTCCCATTTATTTTTAAATAAAAAAAGCTTGAAATGATCACAAAATCTAAAGAAAGAA

Reverse complement sequence

TTCTTTCTTTAGATTTTGTGATCATTTCAAGCTTTTTTTATTTAAAAATAAATGGGAGGGGGGTGTTTTTCTGTAGTTTTTACAAACGTTGTTCAAAACA[C/T]
AGAGTCGAACATGTACCGCTGAAGTGCATTCTGGGTGTCATGGGGCAGAGCCCCATTGGGATGTGTGATCTTGTGTTTTGAGGGGGAGAGGTTGTTGTTA

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 75.30% 3.00% 5.56% 16.17% NA
All Indica  2759 97.20% 0.20% 0.83% 1.78% NA
All Japonica  1512 32.10% 8.50% 14.22% 45.24% NA
Aus  269 98.90% 0.70% 0.00% 0.37% NA
Indica I  595 98.70% 0.20% 0.84% 0.34% NA
Indica II  465 98.90% 0.20% 0.22% 0.65% NA
Indica III  913 95.60% 0.30% 0.66% 3.40% NA
Indica Intermediate  786 96.80% 0.10% 1.40% 1.65% NA
Temperate Japonica  767 32.10% 1.00% 8.34% 58.54% NA
Tropical Japonica  504 31.00% 21.60% 19.44% 27.98% NA
Japonica Intermediate  241 34.40% 4.60% 21.99% 39.00% NA
VI/Aromatic  96 54.20% 4.20% 20.83% 20.83% NA
Intermediate  90 83.30% 0.00% 5.56% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1106988724 G -> A LOC_Os11g12490.1 downstream_gene_variant ; 2845.0bp to feature; MODIFIER silent_mutation Average:30.912; most accessible tissue: Callus, score: 48.908 N N N N
vg1106988724 G -> A LOC_Os11g12510.1 downstream_gene_variant ; 2290.0bp to feature; MODIFIER silent_mutation Average:30.912; most accessible tissue: Callus, score: 48.908 N N N N
vg1106988724 G -> A LOC_Os11g12500.1 intron_variant ; MODIFIER silent_mutation Average:30.912; most accessible tissue: Callus, score: 48.908 N N N N
vg1106988724 G -> DEL N N silent_mutation Average:30.912; most accessible tissue: Callus, score: 48.908 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1106988724 1.24E-06 1.24E-06 mr1098 Jap_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
vg1106988724 8.51E-06 5.78E-07 mr1101 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
vg1106988724 3.34E-06 3.34E-06 mr1589 Jap_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