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Detailed information for vg1126328657:

Variant ID: vg1126328657 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26328657
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


CCACTCAGTACTACTGAGTTTATCGCACTTCTACAATCTACCACTGAAACGGGCTAGCAGGATTAATGAGTGTGTATTCTGTGTATCGACATCGTGATCA[A/G]
CAACCATGAACGATGACAGAGTTGTACATTTTTTCTCACCTTCTCTGCTGATCTACATGTCGCACCAAACTCATAGTTTCTTAACTAAGCACTTTAAAAC

Reverse complement sequence

GTTTTAAAGTGCTTAGTTAAGAAACTATGAGTTTGGTGCGACATGTAGATCAGCAGAGAAGGTGAGAAAAAATGTACAACTCTGTCATCGTTCATGGTTG[T/C]
TGATCACGATGTCGATACACAGAATACACACTCATTAATCCTGCTAGCCCGTTTCAGTGGTAGATTGTAGAAGTGCGATAAACTCAGTAGTACTGAGTGG

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 71.20% 28.80% 0.06% 0.00% NA
All Indica  2759 73.20% 26.70% 0.11% 0.00% NA
All Japonica  1512 66.70% 33.30% 0.00% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 68.60% 31.30% 0.17% 0.00% NA
Indica II  465 84.90% 15.10% 0.00% 0.00% NA
Indica III  913 70.80% 29.10% 0.11% 0.00% NA
Indica Intermediate  786 72.50% 27.40% 0.13% 0.00% NA
Temperate Japonica  767 51.80% 48.20% 0.00% 0.00% NA
Tropical Japonica  504 86.10% 13.90% 0.00% 0.00% NA
Japonica Intermediate  241 73.90% 26.10% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 73.30% 26.70% 0.00% 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
vg1126328657 A -> G LOC_Os11g43650.1 upstream_gene_variant ; 1031.0bp to feature; MODIFIER silent_mutation Average:52.069; most accessible tissue: Zhenshan97 panicle, score: 79.071 N N N N
vg1126328657 A -> G LOC_Os11g43640-LOC_Os11g43650 intergenic_region ; MODIFIER silent_mutation Average:52.069; most accessible tissue: Zhenshan97 panicle, score: 79.071 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126328657 NA 6.82E-07 mr1634 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
vg1126328657 NA 3.63E-07 mr1739 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
vg1126328657 5.97E-07 5.97E-07 mr1819 Ind_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