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Detailed information for vg0122322284:

Variant ID: vg0122322284 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 22322284
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, T: 0.19, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


GTGATAACGCGAAAATTTAAATAAAGCGATAATGCAATAATTTTAAATCAAAATAATTTCACAAAGTGGGATCCAATATGTTCAAAGATGATGTGACTTG[T/C]
CTTGCTCGCTTTCCCAAACGTCGGCTTCAACCTCCACGAAGAGCAGATCTTCCGAAGCTGCAGCGTCTACACGACCAACGGAAAAGAAAAGGGATTTTAC

Reverse complement sequence

GTAAAATCCCTTTTCTTTTCCGTTGGTCGTGTAGACGCTGCAGCTTCGGAAGATCTGCTCTTCGTGGAGGTTGAAGCCGACGTTTGGGAAAGCGAGCAAG[A/G]
CAAGTCACATCATCTTTGAACATATTGGATCCCACTTTGTGAAATTATTTTGATTTAAAATTATTGCATTATCGCTTTATTTAAATTTTCGCGTTATCAC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.50% 41.40% 0.08% 0.00% NA
All Indica  2759 88.10% 11.70% 0.14% 0.00% NA
All Japonica  1512 0.50% 99.50% 0.00% 0.00% NA
Aus  269 71.70% 28.30% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 94.20% 5.80% 0.00% 0.00% NA
Indica III  913 80.70% 19.30% 0.00% 0.00% NA
Indica Intermediate  786 84.40% 15.10% 0.51% 0.00% NA
Temperate Japonica  767 0.00% 100.00% 0.00% 0.00% NA
Tropical Japonica  504 0.40% 99.60% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 48.90% 51.10% 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
vg0122322284 T -> C LOC_Os01g39570.1 upstream_gene_variant ; 573.0bp to feature; MODIFIER silent_mutation Average:25.282; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 N N N N
vg0122322284 T -> C LOC_Os01g39580.1 intron_variant ; MODIFIER silent_mutation Average:25.282; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0122322284 NA 9.55E-06 mr1219 Jap_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
vg0122322284 NA 1.82E-10 mr1819 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
vg0122322284 NA 1.62E-12 mr1138_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
vg0122322284 NA 4.84E-13 mr1191_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
vg0122322284 7.73E-07 NA mr1274_2 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
vg0122322284 3.54E-07 1.39E-07 mr1274_2 Jap_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