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Detailed information for vg1227342757:

Variant ID: vg1227342757 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 27342757
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


GGCCCAAATCTAAAAGCTTACGAGCTGCTTTTGAAGGTTCCAAGGACACCAACATTTGGGATTTCTCCAGAAAAGAAATTGGTGGACAGATTCCTGCAAT[G/A]
CAAATAAGCATATGTTCTTTCAGAGATTTGCAACAGCATTTACTCGTCTGGTTTTAGCAATGCCGACAAGATGGCATAAGGAAATTTATACAGCAAGAAA

Reverse complement sequence

TTTCTTGCTGTATAAATTTCCTTATGCCATCTTGTCGGCATTGCTAAAACCAGACGAGTAAATGCTGTTGCAAATCTCTGAAAGAACATATGCTTATTTG[C/T]
ATTGCAGGAATCTGTCCACCAATTTCTTTTCTGGAGAAATCCCAAATGTTGGTGTCCTTGGAACCTTCAAAAGCAGCTCGTAAGCTTTTAGATTTGGGCC

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 66.70% 33.30% 0.00% 0.00% NA
All Indica  2759 97.80% 2.20% 0.00% 0.00% NA
All Japonica  1512 7.30% 92.70% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 96.70% 3.30% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.40% 0.00% 0.00% NA
Temperate Japonica  767 12.10% 87.90% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.20% 0.00% 0.00% NA
Japonica Intermediate  241 5.40% 94.60% 0.00% 0.00% NA
VI/Aromatic  96 21.90% 78.10% 0.00% 0.00% NA
Intermediate  90 60.00% 40.00% 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
vg1227342757 G -> A LOC_Os12g44090.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:48.596; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N
vg1227342757 G -> A LOC_Os12g44080.1 upstream_gene_variant ; 4977.0bp to feature; MODIFIER silent_mutation Average:48.596; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N
vg1227342757 G -> A LOC_Os12g44100.1 downstream_gene_variant ; 3365.0bp to feature; MODIFIER silent_mutation Average:48.596; 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
vg1227342757 NA 1.23E-28 mr1024 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
vg1227342757 NA 5.10E-32 mr1922 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
vg1227342757 8.88E-06 5.89E-27 mr1024_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
vg1227342757 NA 1.62E-14 mr1162_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
vg1227342757 NA 2.28E-19 mr1657_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
vg1227342757 NA 3.29E-30 mr1891_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
vg1227342757 NA 6.58E-20 mr1922_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