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Detailed information for vg1210106416:

Variant ID: vg1210106416 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 10106416
Reference Allele: GAlternative Allele: T,A
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTATGTCTAATTCCTCGTATATTTATTTTTCTATGATATACGTAAGAGTAAATTGGACAATTCATTATAGATTTTGCATGAATGATGACATGGCATATTC[G/T,A]
TATGATGATTTTGGTGGACCCAAGGACTATTCTATGCCTTATGACAAAGTTTAAGGATTTCTTTAGACCATTTAAAAGGTTAGGGACTAAACTGATATAC

Reverse complement sequence

GTATATCAGTTTAGTCCCTAACCTTTTAAATGGTCTAAAGAAATCCTTAAACTTTGTCATAAGGCATAGAATAGTCCTTGGGTCCACCAAAATCATCATA[C/A,T]
GAATATGCCATGTCATCATTCATGCAAAATCTATAATGAATTGTCCAATTTACTCTTACGTATATCATAGAAAAATAAATATACGAGGAATTAGACATAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.80% 2.70% 0.42% 0.00% A: 0.06%
All Indica  2759 99.60% 0.10% 0.11% 0.00% A: 0.11%
All Japonica  1512 99.90% 0.10% 0.07% 0.00% NA
Aus  269 68.80% 27.10% 4.09% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.60% 0.10% 0.22% 0.00% A: 0.11%
Indica Intermediate  786 99.40% 0.30% 0.13% 0.00% A: 0.25%
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 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 53.10% 43.80% 3.12% 0.00% NA
Intermediate  90 88.90% 8.90% 2.22% 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
vg1210106416 G -> A LOC_Os12g17640.1 upstream_gene_variant ; 820.0bp to feature; MODIFIER silent_mutation Average:43.402; most accessible tissue: Minghui63 flag leaf, score: 68.16 N N N N
vg1210106416 G -> A LOC_Os12g17650.1 upstream_gene_variant ; 640.0bp to feature; MODIFIER silent_mutation Average:43.402; most accessible tissue: Minghui63 flag leaf, score: 68.16 N N N N
vg1210106416 G -> A LOC_Os12g17640-LOC_Os12g17650 intergenic_region ; MODIFIER silent_mutation Average:43.402; most accessible tissue: Minghui63 flag leaf, score: 68.16 N N N N
vg1210106416 G -> T LOC_Os12g17640.1 upstream_gene_variant ; 820.0bp to feature; MODIFIER silent_mutation Average:43.402; most accessible tissue: Minghui63 flag leaf, score: 68.16 N N N N
vg1210106416 G -> T LOC_Os12g17650.1 upstream_gene_variant ; 640.0bp to feature; MODIFIER silent_mutation Average:43.402; most accessible tissue: Minghui63 flag leaf, score: 68.16 N N N N
vg1210106416 G -> T LOC_Os12g17640-LOC_Os12g17650 intergenic_region ; MODIFIER silent_mutation Average:43.402; most accessible tissue: Minghui63 flag leaf, score: 68.16 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1210106416 1.02E-06 8.32E-16 mr1585 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
vg1210106416 NA 1.88E-11 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