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Detailed information for vg0112163580:

Variant ID: vg0112163580 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 12163580
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGTACCGCAGACACCGTGGGTTAATTACTATGGATGAAAACGATACGGAAATTTTCAACCATACCAGCATATTCTGATTATAAAATCTCACTACTATAC[A/T]
TGCTTTTTTTAATACGGCCAAAACACATTTTTGCAGGCAGGCACTTTGCCCACCGTGTTTGGGAAAATTAGAAATTTTCCAGGCAGGCAACCAAACCACA

Reverse complement sequence

TGTGGTTTGGTTGCCTGCCTGGAAAATTTCTAATTTTCCCAAACACGGTGGGCAAAGTGCCTGCCTGCAAAAATGTGTTTTGGCCGTATTAAAAAAAGCA[T/A]
GTATAGTAGTGAGATTTTATAATCAGAATATGCTGGTATGGTTGAAAATTTCCGTATCGTTTTCATCCATAGTAATTAACCCACGGTGTCTGCGGTACAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.90% 2.20% 2.92% 0.00% NA
All Indica  2759 91.60% 3.70% 4.71% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.07% 0.00% NA
Aus  269 98.90% 0.00% 1.12% 0.00% NA
Indica I  595 77.50% 8.10% 14.45% 0.00% NA
Indica II  465 97.20% 0.00% 2.80% 0.00% NA
Indica III  913 95.60% 4.10% 0.33% 0.00% NA
Indica Intermediate  786 94.30% 2.20% 3.56% 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 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 0.00% 4.44% 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
vg0112163580 A -> T LOC_Os01g21670.1 upstream_gene_variant ; 1812.0bp to feature; MODIFIER silent_mutation Average:34.919; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 N N N N
vg0112163580 A -> T LOC_Os01g21690.1 upstream_gene_variant ; 3153.0bp to feature; MODIFIER silent_mutation Average:34.919; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 N N N N
vg0112163580 A -> T LOC_Os01g21680.1 downstream_gene_variant ; 190.0bp to feature; MODIFIER silent_mutation Average:34.919; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 N N N N
vg0112163580 A -> T LOC_Os01g21670-LOC_Os01g21680 intergenic_region ; MODIFIER silent_mutation Average:34.919; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0112163580 NA 2.73E-06 mr1726_2 Ind_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
vg0112163580 NA 5.39E-07 mr1927_2 Ind_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