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Detailed information for vg1227343099:

Variant ID: vg1227343099 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 27343099
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


CCTACAAGATTGTGAGGTGAATGAGCTCGCCAATCTCTGAAGGGATGCCTCCTTGTAGGTAGTTGGCTCTCAAGTAACTGCACACACACAGAGTAAATTA[A/G]
ACCTCCGCATTTCAGCTCTACAAAGTCATTAGCAGACAGATGGAGATGGAACCAAACAAGTACTAGATCGTAGCAGCATACATACATCGCTCTGAGCTCG

Reverse complement sequence

CGAGCTCAGAGCGATGTATGTATGCTGCTACGATCTAGTACTTGTTTGGTTCCATCTCCATCTGTCTGCTAATGACTTTGTAGAGCTGAAATGCGGAGGT[T/C]
TAATTTACTCTGTGTGTGTGCAGTTACTTGAGAGCCAACTACCTACAAGGAGGCATCCCTTCAGAGATTGGCGAGCTCATTCACCTCACAATCTTGTAGG

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 95.50% 4.50% 0.02% 0.00% NA
All Indica  2759 98.70% 1.30% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 37.50% 62.10% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 97.10% 2.90% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1227343099 A -> G LOC_Os12g44100.1 downstream_gene_variant ; 3023.0bp to feature; MODIFIER silent_mutation Average:60.494; most accessible tissue: Zhenshan97 panicle, score: 83.904 N N N N
vg1227343099 A -> G LOC_Os12g44090.1 intron_variant ; MODIFIER silent_mutation Average:60.494; most accessible tissue: Zhenshan97 panicle, score: 83.904 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1227343099 NA 9.58E-14 mr1166 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
vg1227343099 NA 2.61E-21 mr1305_2 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
vg1227343099 NA 1.48E-15 mr1587_2 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