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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0142253896:

Variant ID: vg0142253896 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 42253896
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


CATTGTCTCGTTTTTCTCTATAGACTATTTCTAAGCTAGTAGATAGCTTTGCTCTCTCTCTTCATTTAATATCTTCCAAGTAGAAAAATATGCTAACATG[G/A]
ATCTCTTGTAGAGAGCTTATAGATAACCATTCTTGGTGACCTAATTAATCCTTCTGTTGGAATACATTAATCCTGATCTGGAACATCAACTGAATAATTG

Reverse complement sequence

CAATTATTCAGTTGATGTTCCAGATCAGGATTAATGTATTCCAACAGAAGGATTAATTAGGTCACCAAGAATGGTTATCTATAAGCTCTCTACAAGAGAT[C/T]
CATGTTAGCATATTTTTCTACTTGGAAGATATTAAATGAAGAGAGAGAGCAAAGCTATCTACTAGCTTAGAAATAGTCTATAGAGAAAAACGAGACAATG

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 90.80% 7.80% 1.44% 0.00% NA
All Indica  2759 84.30% 13.20% 2.43% 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 71.30% 22.40% 6.39% 0.00% NA
Indica II  465 87.50% 12.30% 0.22% 0.00% NA
Indica III  913 98.10% 1.50% 0.33% 0.00% NA
Indica Intermediate  786 76.30% 20.50% 3.18% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 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 97.80% 1.10% 1.11% 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
vg0142253896 G -> A LOC_Os01g72850.1 downstream_gene_variant ; 1759.0bp to feature; MODIFIER silent_mutation Average:65.985; most accessible tissue: Zhenshan97 root, score: 81.772 N N N N
vg0142253896 G -> A LOC_Os01g72834.1 intron_variant ; MODIFIER silent_mutation Average:65.985; most accessible tissue: Zhenshan97 root, score: 81.772 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0142253896 NA 7.42E-06 mr1236 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
vg0142253896 NA 7.24E-06 mr1236 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
vg0142253896 NA 1.38E-08 mr1389 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
vg0142253896 NA 3.37E-08 mr1389 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
vg0142253896 NA 3.44E-06 mr1985 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
vg0142253896 1.27E-07 1.27E-07 mr1985 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
vg0142253896 NA 6.30E-09 mr1038_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
vg0142253896 NA 1.80E-08 mr1038_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
vg0142253896 NA 4.75E-07 mr1389_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
vg0142253896 NA 2.43E-07 mr1389_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
vg0142253896 NA 8.31E-06 mr1974_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