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Detailed information for vg0228080650:

Variant ID: vg0228080650 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 28080650
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


TAGAAAGATAGGAAAGGTTGAGCAGTCATTTTGGTGCACTGAACAATTTCGGTTGAGATATGCTTGCCATTTATTAACGACAAGGATAAGGTCACATCAT[G/A]
CAGTCAGTGGATACACTTACTCAGTAGCATCTCACGTAAATCAAGTCAGTCTGTAAGTAAAAGACAACATTAAGATGTTGAACACGACAAGAAACTACAG

Reverse complement sequence

CTGTAGTTTCTTGTCGTGTTCAACATCTTAATGTTGTCTTTTACTTACAGACTGACTTGATTTACGTGAGATGCTACTGAGTAAGTGTATCCACTGACTG[C/T]
ATGATGTGACCTTATCCTTGTCGTTAATAAATGGCAAGCATATCTCAACCGAAATTGTTCAGTGCACCAAAATGACTGCTCAACCTTTCCTATCTTTCTA

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 50.40% 49.10% 0.13% 0.38% NA
All Indica  2759 85.10% 14.10% 0.18% 0.58% NA
All Japonica  1512 0.30% 99.70% 0.00% 0.00% NA
Aus  269 1.90% 97.40% 0.00% 0.74% NA
Indica I  595 96.80% 2.70% 0.34% 0.17% NA
Indica II  465 90.50% 8.80% 0.00% 0.65% NA
Indica III  913 77.20% 22.20% 0.11% 0.44% NA
Indica Intermediate  786 82.30% 16.40% 0.25% 1.02% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 0.40% 99.60% 0.00% 0.00% NA
Japonica Intermediate  241 0.00% 100.00% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 25.60% 73.30% 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
vg0228080650 G -> A LOC_Os02g46080.1 intron_variant ; MODIFIER silent_mutation Average:67.773; most accessible tissue: Callus, score: 83.71 N N N N
vg0228080650 G -> A LOC_Os02g46080.2 intron_variant ; MODIFIER silent_mutation Average:67.773; most accessible tissue: Callus, score: 83.71 N N N N
vg0228080650 G -> DEL N N silent_mutation Average:67.773; most accessible tissue: Callus, score: 83.71 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0228080650 NA 1.58E-51 mr1063 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
vg0228080650 NA 4.59E-50 mr1078 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
vg0228080650 NA 6.05E-54 mr1090 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
vg0228080650 NA 5.94E-49 mr1121 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
vg0228080650 NA 3.13E-48 mr1125 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
vg0228080650 NA 1.43E-15 mr1164 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
vg0228080650 NA 4.35E-42 mr1200 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
vg0228080650 NA 1.55E-31 mr1208 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
vg0228080650 NA 6.75E-28 mr1221 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
vg0228080650 NA 1.09E-29 mr1237 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
vg0228080650 NA 4.00E-20 mr1244 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
vg0228080650 NA 8.29E-28 mr1426 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
vg0228080650 NA 7.42E-07 mr1717 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
vg0228080650 NA 1.55E-42 mr1721 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
vg0228080650 NA 4.99E-11 mr1883 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
vg0228080650 NA 2.32E-15 mr1916 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
vg0228080650 NA 5.91E-53 mr1063_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
vg0228080650 NA 3.50E-62 mr1078_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
vg0228080650 NA 1.56E-37 mr1110_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
vg0228080650 NA 8.12E-62 mr1125_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
vg0228080650 NA 4.10E-23 mr1164_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
vg0228080650 NA 7.43E-26 mr1244_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
vg0228080650 NA 1.73E-17 mr1260_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
vg0228080650 NA 7.91E-13 mr1514_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
vg0228080650 NA 7.11E-31 mr1580_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
vg0228080650 NA 7.33E-11 mr1734_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
vg0228080650 NA 2.13E-29 mr1825_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