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Detailed information for vg0911049759:

Variant ID: vg0911049759 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 11049759
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.87, A: 0.13, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:


ATAACTTATTTTGTTTTATAATCGCTTCTGTTACTGAATTGTTATTCAATTCTTTTTGCGTGCTACAAGGCAAGATGACACTTGGGGGCAAACCTCCCTC[A/G]
TAGCCTCCTAGGTTGATGGGGTGACCACCTACGGTGCATGTCTCGTGGCATTACTCCACATATTTTTTTTCGTGGCACCCCAAACGCTCCCACATATTTG

Reverse complement sequence

CAAATATGTGGGAGCGTTTGGGGTGCCACGAAAAAAAATATGTGGAGTAATGCCACGAGACATGCACCGTAGGTGGTCACCCCATCAACCTAGGAGGCTA[T/C]
GAGGGAGGTTTGCCCCCAAGTGTCATCTTGCCTTGTAGCACGCAAAAAGAATTGAATAACAATTCAGTAACAGAAGCGATTATAAAACAAAATAAGTTAT

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 31.70% 14.20% 1.21% 52.88% NA
All Indica  2759 4.20% 7.80% 1.85% 86.15% NA
All Japonica  1512 84.10% 13.20% 0.07% 2.58% NA
Aus  269 3.30% 77.30% 1.86% 17.47% NA
Indica I  595 10.80% 3.20% 1.51% 84.54% NA
Indica II  465 2.80% 9.90% 1.08% 86.24% NA
Indica III  913 1.10% 10.30% 1.64% 86.97% NA
Indica Intermediate  786 3.60% 7.30% 2.80% 86.39% NA
Temperate Japonica  767 86.20% 13.00% 0.00% 0.78% NA
Tropical Japonica  504 88.90% 5.40% 0.20% 5.56% NA
Japonica Intermediate  241 67.60% 30.30% 0.00% 2.07% NA
VI/Aromatic  96 50.00% 40.60% 0.00% 9.38% NA
Intermediate  90 60.00% 10.00% 0.00% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0911049759 A -> G LOC_Os09g18020-LOC_Os09g18040 intergenic_region ; MODIFIER silent_mutation Average:11.899; most accessible tissue: Callus, score: 71.679 N N N N
vg0911049759 A -> DEL N N silent_mutation Average:11.899; most accessible tissue: Callus, score: 71.679 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0911049759 NA 4.74E-06 mr1305 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
vg0911049759 NA 2.87E-06 mr1365 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
vg0911049759 2.09E-07 2.09E-07 mr1385 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
vg0911049759 NA 1.98E-06 mr1585 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
vg0911049759 NA 4.88E-06 mr1586 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
vg0911049759 8.12E-06 8.11E-06 mr1643 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