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Detailed information for vg0816239139:

Variant ID: vg0816239139 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 16239139
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


GCCGCAGAAGTATGTACTGCTCATGCATCTGTACTGTTCAGAAAACAAAATGTATTTTAGATAGGCTGGCAACAATCACGAGAACAATTCCACTTAAATT[G/T]
CTCTGTTGATCCCAAAGTTTCAGAACAAGAGCTAAATCTCAAGTAGAAAAAGCTCCTGGGAGAACTCAATGATGAAGAAAATACAAATGCAAAATATTTA

Reverse complement sequence

TAAATATTTTGCATTTGTATTTTCTTCATCATTGAGTTCTCCCAGGAGCTTTTTCTACTTGAGATTTAGCTCTTGTTCTGAAACTTTGGGATCAACAGAG[C/A]
AATTTAAGTGGAATTGTTCTCGTGATTGTTGCCAGCCTATCTAAAATACATTTTGTTTTCTGAACAGTACAGATGCATGAGCAGTACATACTTCTGCGGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.50% 3.90% 0.83% 8.80% NA
All Indica  2759 92.50% 6.30% 0.87% 0.25% NA
All Japonica  1512 74.00% 0.20% 0.79% 25.00% NA
Aus  269 90.00% 0.00% 1.12% 8.92% NA
Indica I  595 98.50% 0.00% 1.18% 0.34% NA
Indica II  465 92.70% 5.60% 1.29% 0.43% NA
Indica III  913 88.10% 11.10% 0.77% 0.11% NA
Indica Intermediate  786 93.10% 6.10% 0.51% 0.25% NA
Temperate Japonica  767 97.80% 0.00% 0.13% 2.09% NA
Tropical Japonica  504 49.40% 0.60% 1.98% 48.02% NA
Japonica Intermediate  241 49.80% 0.00% 0.41% 49.79% NA
VI/Aromatic  96 95.80% 0.00% 0.00% 4.17% NA
Intermediate  90 90.00% 6.70% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0816239139 G -> T LOC_Os08g26700.1 missense_variant ; p.Gln121Lys; MODERATE nonsynonymous_codon ; Q121K Average:36.569; most accessible tissue: Zhenshan97 panicle, score: 52.263 unknown unknown DELETERIOUS 0.00
vg0816239139 G -> DEL LOC_Os08g26700.1 N frameshift_variant Average:36.569; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0816239139 9.58E-07 3.01E-08 mr1090 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
vg0816239139 3.48E-06 NA mr1111 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
vg0816239139 2.75E-06 1.36E-06 mr1121 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
vg0816239139 1.53E-06 5.03E-08 mr1211 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
vg0816239139 2.47E-07 NA mr1068_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
vg0816239139 2.77E-09 4.68E-09 mr1090_2 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
vg0816239139 5.26E-07 NA mr1094_2 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
vg0816239139 5.89E-06 NA mr1096_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
vg0816239139 4.76E-07 NA mr1111_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
vg0816239139 1.85E-07 2.66E-07 mr1121_2 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
vg0816239139 5.10E-07 NA mr1144_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
vg0816239139 6.82E-09 5.94E-10 mr1211_2 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