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Detailed information for vg0133425349:

Variant ID: vg0133425349 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 33425349
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


GAGAGGAACCCAAAATACAAGAAAAATACCCCGAGGAGAAACCCGGGTCGCGTCCTCCGGCCCAGAGTAGTCAAAGGTTGGATGGGCTCGAGCCTGGAGC[G/A]
GCTGGAGCCGTCTAACAATGAAGTCGGCAGCGACTTCATATCCCGACAACCCCTGTACTCAGAGGTCATCAATGATATCGATGAAAGATTGGAGGGATGG

Reverse complement sequence

CCATCCCTCCAATCTTTCATCGATATCATTGATGACCTCTGAGTACAGGGGTTGTCGGGATATGAAGTCGCTGCCGACTTCATTGTTAGACGGCTCCAGC[C/T]
GCTCCAGGCTCGAGCCCATCCAACCTTTGACTACTCTGGGCCGGAGGACGCGACCCGGGTTTCTCCTCGGGGTATTTTTCTTGTATTTTGGGTTCCTCTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.80% 39.10% 3.47% 0.66% NA
All Indica  2759 92.40% 6.80% 0.80% 0.04% NA
All Japonica  1512 1.10% 98.90% 0.00% 0.00% NA
Aus  269 34.90% 2.20% 52.04% 10.78% NA
Indica I  595 93.10% 6.90% 0.00% 0.00% NA
Indica II  465 97.20% 2.60% 0.22% 0.00% NA
Indica III  913 92.20% 7.70% 0.11% 0.00% NA
Indica Intermediate  786 89.10% 8.30% 2.54% 0.13% NA
Temperate Japonica  767 0.90% 99.10% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 25.60% 71.10% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0133425349 G -> A LOC_Os01g57800.1 upstream_gene_variant ; 3252.0bp to feature; MODIFIER silent_mutation Average:55.808; most accessible tissue: Zhenshan97 flag leaf, score: 72.012 N N N N
vg0133425349 G -> A LOC_Os01g57780.1 downstream_gene_variant ; 4987.0bp to feature; MODIFIER silent_mutation Average:55.808; most accessible tissue: Zhenshan97 flag leaf, score: 72.012 N N N N
vg0133425349 G -> A LOC_Os01g57790.1 intron_variant ; MODIFIER silent_mutation Average:55.808; most accessible tissue: Zhenshan97 flag leaf, score: 72.012 N N N N
vg0133425349 G -> DEL N N silent_mutation Average:55.808; most accessible tissue: Zhenshan97 flag leaf, score: 72.012 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0133425349 NA 1.16E-24 mr1003 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
vg0133425349 1.31E-10 NA mr1008 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
vg0133425349 1.30E-09 6.18E-17 mr1008 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
vg0133425349 8.84E-12 NA mr1009 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
vg0133425349 1.12E-10 2.08E-17 mr1009 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
vg0133425349 NA 9.10E-06 mr1014 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
vg0133425349 4.03E-06 NA mr1015 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
vg0133425349 6.84E-06 1.84E-07 mr1015 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
vg0133425349 NA 1.91E-23 mr1051 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
vg0133425349 NA 2.45E-13 mr1170 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
vg0133425349 NA 7.11E-08 mr1559 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
vg0133425349 NA 4.93E-15 mr1713 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
vg0133425349 NA 4.12E-28 mr1793 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
vg0133425349 1.96E-09 NA mr1008_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
vg0133425349 1.54E-10 5.28E-19 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
vg0133425349 1.45E-06 NA mr1015_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
vg0133425349 NA 4.58E-08 mr1015_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
vg0133425349 NA 2.39E-28 mr1051_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
vg0133425349 NA 1.31E-09 mr1322_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
vg0133425349 NA 7.69E-14 mr1326_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
vg0133425349 NA 3.00E-08 mr1527_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