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Detailed information for vg1103239153:

Variant ID: vg1103239153 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 3239153
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.55, A: 0.44, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


GGTCTATGCATTGGCTTCGAACTCCAGTCCTAGGCCTTGACGAGGCCTTCTAGCTCCACATTTTGTTTTGCTTTTCTCAGTTTGGGTCCTCTCTTCTCTT[A/G]
TTTGGTGTGTTCAACTTGTCTTGAACTACACTCTCTTCTGGAGTGAATCTTTGTAATAATTGGCTGTAGTTCTTTTTGAACAAAGGCCGGGATATTATAT

Reverse complement sequence

ATATAATATCCCGGCCTTTGTTCAAAAAGAACTACAGCCAATTATTACAAAGATTCACTCCAGAAGAGAGTGTAGTTCAAGACAAGTTGAACACACCAAA[T/C]
AAGAGAAGAGAGGACCCAAACTGAGAAAAGCAAAACAAAATGTGGAGCTAGAAGGCCTCGTCAAGGCCTAGGACTGGAGTTCGAAGCCAATGCATAGACC

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 68.90% 31.10% 0.04% 0.00% NA
All Indica  2759 98.00% 2.00% 0.04% 0.00% NA
All Japonica  1512 10.40% 89.60% 0.07% 0.00% NA
Aus  269 95.90% 4.10% 0.00% 0.00% NA
Indica I  595 97.50% 2.50% 0.00% 0.00% NA
Indica II  465 98.70% 1.10% 0.22% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 96.40% 3.60% 0.00% 0.00% NA
Temperate Japonica  767 2.60% 97.40% 0.00% 0.00% NA
Tropical Japonica  504 23.20% 76.80% 0.00% 0.00% NA
Japonica Intermediate  241 8.30% 91.30% 0.41% 0.00% NA
VI/Aromatic  96 82.30% 17.70% 0.00% 0.00% NA
Intermediate  90 64.40% 35.60% 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
vg1103239153 A -> G LOC_Os11g06650.1 upstream_gene_variant ; 2607.0bp to feature; MODIFIER silent_mutation Average:28.605; most accessible tissue: Zhenshan97 panicle, score: 43.098 N N N N
vg1103239153 A -> G LOC_Os11g06660.1 downstream_gene_variant ; 4857.0bp to feature; MODIFIER silent_mutation Average:28.605; most accessible tissue: Zhenshan97 panicle, score: 43.098 N N N N
vg1103239153 A -> G LOC_Os11g06650-LOC_Os11g06660 intergenic_region ; MODIFIER silent_mutation Average:28.605; most accessible tissue: Zhenshan97 panicle, score: 43.098 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1103239153 NA 1.61E-12 mr1170 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
vg1103239153 4.68E-06 NA mr1608 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
vg1103239153 NA 3.00E-06 mr1558_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
vg1103239153 NA 6.66E-06 mr1662_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