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Detailed information for vg0125460306:

Variant ID: vg0125460306 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 25460306
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGGATACAATATTTTCCTTTAGAGGGTGGGATATTATTTCCCTATTTCATTTTATCGACGTTTGATGTCTCGACTACAGTATTTGCATGGCATGGGGAT[C/T]
GTTGGTACTAGGGTATACGCAAGACTGAGGTAAAAGAGATGGAGACGAGGATTTTTATACAGGTTCGGGCCCCTGAATTGTCAGGTAATAACCCTACATC

Reverse complement sequence

GATGTAGGGTTATTACCTGACAATTCAGGGGCCCGAACCTGTATAAAAATCCTCGTCTCCATCTCTTTTACCTCAGTCTTGCGTATACCCTAGTACCAAC[G/A]
ATCCCCATGCCATGCAAATACTGTAGTCGAGACATCAAACGTCGATAAAATGAAATAGGGAAATAATATCCCACCCTCTAAAGGAAAATATTGTATCCTA

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 95.30% 4.70% 0.00% 0.00% NA
All Indica  2759 92.30% 7.70% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.60% 3.40% 0.00% 0.00% NA
Indica II  465 95.50% 4.50% 0.00% 0.00% NA
Indica III  913 89.60% 10.40% 0.00% 0.00% NA
Indica Intermediate  786 90.20% 9.80% 0.00% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0125460306 C -> T LOC_Os01g44380.1 upstream_gene_variant ; 762.0bp to feature; MODIFIER silent_mutation Average:39.224; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0125460306 C -> T LOC_Os01g44390.2 upstream_gene_variant ; 1697.0bp to feature; MODIFIER silent_mutation Average:39.224; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0125460306 C -> T LOC_Os01g44390.1 upstream_gene_variant ; 1685.0bp to feature; MODIFIER silent_mutation Average:39.224; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0125460306 C -> T LOC_Os01g44370.1 downstream_gene_variant ; 2444.0bp to feature; MODIFIER silent_mutation Average:39.224; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0125460306 C -> T LOC_Os01g44380-LOC_Os01g44390 intergenic_region ; MODIFIER silent_mutation Average:39.224; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0125460306 NA 1.07E-06 mr1064 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
vg0125460306 NA 8.63E-06 mr1534 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
vg0125460306 8.98E-07 8.98E-07 mr1832 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