Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg1102804893:

Variant ID: vg1102804893 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 2804893
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: 309. )

Flanking Sequence (100 bp) in Reference Genome:


ACATCCCCTCCTAAGGCATCTTAGGCCTCACACAGAGGCCACATGCGCCATGCTTGGCTCTTATACAACCCTCCCTCCAGAACTCCAACCCAGCCACACA[G/A]
ACATCTTGTACAACCCTCCCTGTGTGAGGCCACATGCGCCATGCTCGGCTCTTGTACAACCCTCCCTGCTCCAACCCAGCCACACAGACATCTTGTACAA

Reverse complement sequence

TTGTACAAGATGTCTGTGTGGCTGGGTTGGAGCAGGGAGGGTTGTACAAGAGCCGAGCATGGCGCATGTGGCCTCACACAGGGAGGGTTGTACAAGATGT[C/T]
TGTGTGGCTGGGTTGGAGTTCTGGAGGGAGGGTTGTATAAGAGCCAAGCATGGCGCATGTGGCCTCTGTGTGAGGCCTAAGATGCCTTAGGAGGGGATGT

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 97.50% 1.20% 1.29% 0.00% NA
All Indica  2759 99.20% 0.10% 0.76% 0.00% NA
All Japonica  1512 94.00% 3.60% 2.45% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 96.50% 0.30% 3.19% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.00% 0.25% 0.00% NA
Temperate Japonica  767 97.50% 0.10% 2.35% 0.00% NA
Tropical Japonica  504 97.00% 2.80% 0.20% 0.00% NA
Japonica Intermediate  241 76.30% 16.20% 7.47% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg1102804893 G -> A LOC_Os11g05940.1 upstream_gene_variant ; 2672.0bp to feature; MODIFIER silent_mutation Average:67.876; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N
vg1102804893 G -> A LOC_Os11g05950.1 downstream_gene_variant ; 2715.0bp to feature; MODIFIER silent_mutation Average:67.876; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N
vg1102804893 G -> A LOC_Os11g05960.1 downstream_gene_variant ; 4764.0bp to feature; MODIFIER silent_mutation Average:67.876; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N
vg1102804893 G -> A LOC_Os11g05940-LOC_Os11g05950 intergenic_region ; MODIFIER silent_mutation Average:67.876; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1102804893 2.81E-06 NA mr1364 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
vg1102804893 2.35E-06 NA mr1443 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
vg1102804893 NA 1.89E-06 mr1496_2 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