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Detailed information for vg0131923446:

Variant ID: vg0131923446 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 31923446
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


CCTAGGGCTGCTTGGGTTGAGCCCTAGGCTTGCCTCCATAATCATGCTTAAATTCTCTTAATTCACCATGTAATTTTTCGAGGAAAATACTCCATTAGTT[G/A]
AGCCCTACTTAGCCTTTGGCTTTGATAATTTCTTGCTCCGCCAACTGCAAAAAACGTTTTGGGAAGTAGTTTGAGAGAGTGATGTTTAGTCAGACAAACA

Reverse complement sequence

TGTTTGTCTGACTAAACATCACTCTCTCAAACTACTTCCCAAAACGTTTTTTGCAGTTGGCGGAGCAAGAAATTATCAAAGCCAAAGGCTAAGTAGGGCT[C/T]
AACTAATGGAGTATTTTCCTCGAAAAATTACATGGTGAATTAAGAGAATTTAAGCATGATTATGGAGGCAAGCCTAGGGCTCAACCCAAGCAGCCCTAGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.50% 1.40% 0.17% 0.00% NA
All Indica  2759 97.40% 2.30% 0.29% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 88.60% 10.10% 1.34% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0131923446 G -> A LOC_Os01g55420.1 upstream_gene_variant ; 2420.0bp to feature; MODIFIER silent_mutation Average:69.198; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0131923446 G -> A LOC_Os01g55410.1 downstream_gene_variant ; 1040.0bp to feature; MODIFIER silent_mutation Average:69.198; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0131923446 G -> A LOC_Os01g55430.1 downstream_gene_variant ; 3688.0bp to feature; MODIFIER silent_mutation Average:69.198; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0131923446 G -> A LOC_Os01g55430.2 downstream_gene_variant ; 3690.0bp to feature; MODIFIER silent_mutation Average:69.198; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0131923446 G -> A LOC_Os01g55410-LOC_Os01g55420 intergenic_region ; MODIFIER silent_mutation Average:69.198; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0131923446 3.78E-06 3.78E-06 mr1469 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
vg0131923446 NA 4.60E-07 mr1728 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
vg0131923446 NA 3.76E-06 mr1798 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
vg0131923446 NA 5.09E-06 mr1860 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
vg0131923446 NA 1.30E-06 mr1008_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