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Detailed information for vg0623662680:

Variant ID: vg0623662680 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 23662680
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.75, C: 0.27, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:


AGTCTGATCATGTATGCATATATTTTTAAATTTGGATAGAATCTGTGCTTTCTTTCGGCATCATCCGAAAGTGAGCTGAGCTATACAGAAATATGATATG[C/T]
TGAAAGTAAATAGCCATGTTGTTTTTCTCCCTATGTAATCTGCAGATGCGATCATTAGTAATCAGTGAATTAAGCAGGAACCTGTCACGCCAGAAGCTAC

Reverse complement sequence

GTAGCTTCTGGCGTGACAGGTTCCTGCTTAATTCACTGATTACTAATGATCGCATCTGCAGATTACATAGGGAGAAAAACAACATGGCTATTTACTTTCA[G/A]
CATATCATATTTCTGTATAGCTCAGCTCACTTTCGGATGATGCCGAAAGAAAGCACAGATTCTATCCAAATTTAAAAATATATGCATACATGATCAGACT

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 51.50% 48.40% 0.04% 0.00% NA
All Indica  2759 29.00% 70.90% 0.07% 0.00% NA
All Japonica  1512 99.00% 1.00% 0.00% 0.00% NA
Aus  269 1.10% 98.90% 0.00% 0.00% NA
Indica I  595 76.10% 23.90% 0.00% 0.00% NA
Indica II  465 9.90% 90.10% 0.00% 0.00% NA
Indica III  913 13.60% 86.30% 0.11% 0.00% NA
Indica Intermediate  786 22.50% 77.40% 0.13% 0.00% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 82.30% 17.70% 0.00% 0.00% NA
Intermediate  90 62.20% 37.80% 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
vg0623662680 C -> T LOC_Os06g39840.1 upstream_gene_variant ; 488.0bp to feature; MODIFIER silent_mutation Average:40.605; most accessible tissue: Callus, score: 73.989 N N N N
vg0623662680 C -> T LOC_Os06g39820.1 downstream_gene_variant ; 1691.0bp to feature; MODIFIER silent_mutation Average:40.605; most accessible tissue: Callus, score: 73.989 N N N N
vg0623662680 C -> T LOC_Os06g39830.1 intron_variant ; MODIFIER silent_mutation Average:40.605; most accessible tissue: Callus, score: 73.989 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0623662680 NA 4.15E-07 mr1510 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
vg0623662680 6.75E-07 NA mr1566 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
vg0623662680 NA 5.37E-07 mr1602 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
vg0623662680 NA 1.34E-06 mr1821 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
vg0623662680 9.39E-06 5.10E-06 mr1844 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