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Detailed information for vg0906318181:

Variant ID: vg0906318181 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6318181
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTCCAATAAGGACTTTATGTTTTCCTTTTATCTTTAGGAAAGTTTCTTTCTTGTCCTACAAGGACTAGTATCTCCCCATGGGTATAAATATGTACACCT[G/A]
GGGTCATTGTTATAGATCTCTCCACAATCAATACAATTTGGCGCATCGCCACCTTTTTATGTTTTCTACTTTTTATTATCCGGCGGAACATGGAACCTGA

Reverse complement sequence

TCAGGTTCCATGTTCCGCCGGATAATAAAAAGTAGAAAACATAAAAAGGTGGCGATGCGCCAAATTGTATTGATTGTGGAGAGATCTATAACAATGACCC[C/T]
AGGTGTACATATTTATACCCATGGGGAGATACTAGTCCTTGTAGGACAAGAAAGAAACTTTCCTAAAGATAAAAGGAAAACATAAAGTCCTTATTGGACA

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 87.10% 4.90% 0.63% 7.36% NA
All Indica  2759 91.90% 2.50% 0.87% 4.78% NA
All Japonica  1512 86.60% 0.10% 0.26% 13.03% NA
Aus  269 52.40% 41.30% 0.74% 5.58% NA
Indica I  595 93.10% 0.00% 0.84% 6.05% NA
Indica II  465 98.10% 1.70% 0.00% 0.22% NA
Indica III  913 91.90% 3.40% 0.66% 4.05% NA
Indica Intermediate  786 87.30% 3.70% 1.65% 7.38% NA
Temperate Japonica  767 94.80% 0.00% 0.00% 5.22% NA
Tropical Japonica  504 86.10% 0.00% 0.20% 13.69% NA
Japonica Intermediate  241 61.80% 0.40% 1.24% 36.51% NA
VI/Aromatic  96 55.20% 44.80% 0.00% 0.00% NA
Intermediate  90 85.60% 10.00% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0906318181 G -> DEL N N silent_mutation Average:40.74; most accessible tissue: Zhenshan97 young leaf, score: 57.159 N N N N
vg0906318181 G -> A LOC_Os09g11360-LOC_Os09g11370 intergenic_region ; MODIFIER silent_mutation Average:40.74; most accessible tissue: Zhenshan97 young leaf, score: 57.159 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906318181 NA 3.02E-06 mr1189 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
vg0906318181 2.93E-06 NA mr1337 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
vg0906318181 NA 2.81E-09 mr1570 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
vg0906318181 NA 2.89E-06 mr1684 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
vg0906318181 NA 7.85E-08 mr1705 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
vg0906318181 NA 1.55E-06 mr1734 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
vg0906318181 NA 8.85E-07 mr1808 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
vg0906318181 NA 2.39E-07 mr1585_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