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Detailed information for vg0234310846:

Variant ID: vg0234310846 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 34310846
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, C: 0.10, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


ATATTAGAAAACCGGCCTCTACATCCACGACAAGTACATTTACATGTACCTATGAAGATAATATACCTATACCTATGGAATTCCTCTACTTATTCTACTG[T/C]
AGTTGGTAATTTTCTTCATTTTTTTTAAGATAATGAAATAACATTCCGGCTTTTGCTCAACGAGATACAACCAATTATTACAAAGTCCACACACGAACAA

Reverse complement sequence

TTGTTCGTGTGTGGACTTTGTAATAATTGGTTGTATCTCGTTGAGCAAAAGCCGGAATGTTATTTCATTATCTTAAAAAAAATGAAGAAAATTACCAACT[A/G]
CAGTAGAATAAGTAGAGGAATTCCATAGGTATAGGTATATTATCTTCATAGGTACATGTAAATGTACTTGTCGTGGATGTAGAGGCCGGTTTTCTAATAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.80% 47.90% 0.28% 0.00% NA
All Indica  2759 28.40% 71.20% 0.40% 0.00% NA
All Japonica  1512 94.00% 6.00% 0.07% 0.00% NA
Aus  269 59.50% 40.50% 0.00% 0.00% NA
Indica I  595 44.40% 54.80% 0.84% 0.00% NA
Indica II  465 14.00% 85.80% 0.22% 0.00% NA
Indica III  913 21.00% 78.80% 0.22% 0.00% NA
Indica Intermediate  786 33.30% 66.30% 0.38% 0.00% NA
Temperate Japonica  767 97.50% 2.50% 0.00% 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 55.60% 43.30% 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
vg0234310846 T -> C LOC_Os02g56040.1 upstream_gene_variant ; 3117.0bp to feature; MODIFIER silent_mutation Average:39.339; most accessible tissue: Callus, score: 59.39 N N N N
vg0234310846 T -> C LOC_Os02g56060.1 upstream_gene_variant ; 1860.0bp to feature; MODIFIER silent_mutation Average:39.339; most accessible tissue: Callus, score: 59.39 N N N N
vg0234310846 T -> C LOC_Os02g56050.1 intron_variant ; MODIFIER silent_mutation Average:39.339; most accessible tissue: Callus, score: 59.39 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0234310846 NA 3.63E-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
vg0234310846 NA 6.09E-06 mr1293_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
vg0234310846 NA 2.52E-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
vg0234310846 NA 2.13E-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
vg0234310846 NA 4.60E-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
vg0234310846 NA 2.71E-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
vg0234310846 NA 1.73E-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
vg0234310846 NA 8.16E-10 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
vg0234310846 NA 1.53E-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
vg0234310846 NA 5.58E-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
vg0234310846 NA 5.22E-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
vg0234310846 NA 1.01E-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