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Detailed information for vg0234310744:

Variant ID: vg0234310744 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 34310744
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.06, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


GCAACCTTTATAGCCTCTAATGCTTGAAGGCAGCCGATTACTCCTGGAACTAACAAACAAAAATGTAGACATTGGATCATTCATATAGACAATATGGATG[G/A]
GATATTAGAAAACCGGCCTCTACATCCACGACAAGTACATTTACATGTACCTATGAAGATAATATACCTATACCTATGGAATTCCTCTACTTATTCTACT

Reverse complement sequence

AGTAGAATAAGTAGAGGAATTCCATAGGTATAGGTATATTATCTTCATAGGTACATGTAAATGTACTTGTCGTGGATGTAGAGGCCGGTTTTCTAATATC[C/T]
CATCCATATTGTCTATATGAATGATCCAATGTCTACATTTTTGTTTGTTAGTTCCAGGAGTAATCGGCTGCCTTCAAGCATTAGAGGCTATAAAGGTTGC

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 51.70% 47.80% 0.42% 0.02% NA
All Indica  2759 28.30% 71.10% 0.54% 0.04% NA
All Japonica  1512 94.00% 5.90% 0.13% 0.00% NA
Aus  269 60.20% 39.80% 0.00% 0.00% NA
Indica I  595 44.40% 54.60% 1.01% 0.00% NA
Indica II  465 13.80% 86.00% 0.22% 0.00% NA
Indica III  913 21.00% 78.60% 0.22% 0.11% NA
Indica Intermediate  786 33.10% 66.20% 0.76% 0.00% NA
Temperate Japonica  767 97.50% 2.30% 0.13% 0.00% NA
Tropical Japonica  504 88.70% 11.10% 0.20% 0.00% NA
Japonica Intermediate  241 93.80% 6.20% 0.00% 0.00% NA
VI/Aromatic  96 34.40% 65.60% 0.00% 0.00% NA
Intermediate  90 54.40% 42.20% 3.33% 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
vg0234310744 G -> A LOC_Os02g56040.1 upstream_gene_variant ; 3015.0bp to feature; MODIFIER silent_mutation Average:43.899; most accessible tissue: Callus, score: 83.15 N N N N
vg0234310744 G -> A LOC_Os02g56060.1 upstream_gene_variant ; 1962.0bp to feature; MODIFIER silent_mutation Average:43.899; most accessible tissue: Callus, score: 83.15 N N N N
vg0234310744 G -> A LOC_Os02g56050.1 intron_variant ; MODIFIER silent_mutation Average:43.899; most accessible tissue: Callus, score: 83.15 N N N N
vg0234310744 G -> DEL N N silent_mutation Average:43.899; most accessible tissue: Callus, score: 83.15 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0234310744 NA 7.61E-06 mr1041_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
vg0234310744 NA 3.50E-06 mr1294_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
vg0234310744 NA 3.84E-08 mr1418_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
vg0234310744 NA 6.39E-06 mr1420_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
vg0234310744 NA 4.23E-07 mr1488_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
vg0234310744 NA 2.22E-06 mr1497_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
vg0234310744 NA 1.16E-09 mr1506_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
vg0234310744 NA 3.00E-07 mr1604_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
vg0234310744 NA 5.14E-10 mr1659_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
vg0234310744 NA 7.06E-06 mr1779_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
vg0234310744 NA 1.73E-06 mr1992_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