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Detailed information for vg1127963105:

Variant ID: vg1127963105 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27963105
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.88, G: 0.12, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:


TATTGCATTTATTTTCGAATGTCATTGGGTGAAATTAACCTATTGTTTGCTAAAGCCCTTTTGTTCTTGATTACTTTATTCCTTGATACCTTGGGTTAAT[G/A]
TAACTTGACTAGTTGAACTTTATATATATTGGTTCAACTAGAATTTATATATGATTGCTTAGCCCTGCTTAGAAACATTAGCACACTATTGGGATAACTT

Reverse complement sequence

AAGTTATCCCAATAGTGTGCTAATGTTTCTAAGCAGGGCTAAGCAATCATATATAAATTCTAGTTGAACCAATATATATAAAGTTCAACTAGTCAAGTTA[C/T]
ATTAACCCAAGGTATCAAGGAATAAAGTAATCAAGAACAAAAGGGCTTTAGCAAACAATAGGTTAATTTCACCCAATGACATTCGAAAATAAATGCAATA

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 46.00% 26.40% 10.66% 16.89% NA
All Indica  2759 64.30% 17.60% 10.58% 7.54% NA
All Japonica  1512 11.80% 38.00% 12.30% 37.83% NA
Aus  269 46.10% 47.20% 4.09% 2.60% NA
Indica I  595 64.00% 16.00% 11.60% 8.40% NA
Indica II  465 53.10% 11.80% 18.49% 16.56% NA
Indica III  913 74.20% 18.20% 5.26% 2.41% NA
Indica Intermediate  786 59.50% 21.60% 11.32% 7.51% NA
Temperate Japonica  767 5.00% 27.50% 7.04% 60.50% NA
Tropical Japonica  504 21.60% 53.00% 17.06% 8.33% NA
Japonica Intermediate  241 13.30% 40.20% 19.09% 27.39% NA
VI/Aromatic  96 66.70% 22.90% 6.25% 4.17% NA
Intermediate  90 37.80% 44.40% 10.00% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127963105 G -> A LOC_Os11g46150-LOC_Os11g46180 intergenic_region ; MODIFIER silent_mutation Average:13.288; most accessible tissue: Minghui63 young leaf, score: 20.156 N N N N
vg1127963105 G -> DEL N N silent_mutation Average:13.288; most accessible tissue: Minghui63 young leaf, score: 20.156 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127963105 NA 6.92E-06 mr1075 Ind_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
vg1127963105 3.80E-06 2.03E-10 mr1299 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
vg1127963105 6.07E-06 6.07E-06 mr1299 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
vg1127963105 NA 5.80E-06 mr1304 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
vg1127963105 NA 2.46E-08 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
vg1127963105 NA 4.83E-06 mr1427 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
vg1127963105 NA 7.35E-06 mr1634 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
vg1127963105 NA 5.13E-06 mr1724 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
vg1127963105 NA 2.31E-06 mr1727 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