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Detailed information for vg0411669926:

Variant ID: vg0411669926 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 11669926
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: 0.07, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:


ATCATTATTGCTTTCCTTCCGAGAGTCCCCTTTCCCCGTAGTCTCCCTTTATGGCGTGATTCAGGTATCCCGATTGGGCGATGCTTGCCTCTGGACGAGC[G/A]
CGGTTACGAACATACTTCTTCAGAACGCCCATGTACTTCTTGAAAGGAAACATGTTGTGTAGGTACACAGGACCGAGAATACCGATCTCTTTGACAAGGT

Reverse complement sequence

ACCTTGTCAAAGAGATCGGTATTCTCGGTCCTGTGTACCTACACAACATGTTTCCTTTCAAGAAGTACATGGGCGTTCTGAAGAAGTATGTTCGTAACCG[C/T]
GCTCGTCCAGAGGCAAGCATCGCCCAATCGGGATACCTGAATCACGCCATAAAGGGAGACTACGGGGAAAGGGGACTCTCGGAAGGAAAGCAATAATGAT

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 30.20% 5.70% 6.47% 57.62% NA
All Indica  2759 2.20% 0.20% 7.58% 90.00% NA
All Japonica  1512 87.40% 11.60% 0.13% 0.86% NA
Aus  269 1.10% 0.00% 31.97% 66.91% NA
Indica I  595 1.30% 0.20% 1.01% 97.48% NA
Indica II  465 4.90% 0.20% 13.33% 81.51% NA
Indica III  913 1.30% 0.00% 10.19% 88.50% NA
Indica Intermediate  786 2.40% 0.40% 6.11% 91.09% NA
Temperate Japonica  767 92.00% 7.60% 0.00% 0.39% NA
Tropical Japonica  504 89.90% 8.70% 0.20% 1.19% NA
Japonica Intermediate  241 67.20% 30.70% 0.41% 1.66% NA
VI/Aromatic  96 6.20% 79.20% 5.21% 9.38% NA
Intermediate  90 38.90% 14.40% 4.44% 42.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0411669926 G -> DEL N N silent_mutation Average:12.197; most accessible tissue: Callus, score: 25.707 N N N N
vg0411669926 G -> A LOC_Os04g20800.1 upstream_gene_variant ; 3470.0bp to feature; MODIFIER silent_mutation Average:12.197; most accessible tissue: Callus, score: 25.707 N N N N
vg0411669926 G -> A LOC_Os04g20790.1 intron_variant ; MODIFIER silent_mutation Average:12.197; most accessible tissue: Callus, score: 25.707 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0411669926 7.83E-07 1.15E-08 mr1343 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
vg0411669926 5.17E-07 9.70E-13 mr1829 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
vg0411669926 7.80E-08 8.02E-17 mr1842 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
vg0411669926 NA 1.80E-06 mr1549_2 Jap_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
vg0411669926 NA 1.03E-06 mr1567_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
vg0411669926 NA 4.58E-14 mr1829_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
vg0411669926 9.69E-06 3.76E-17 mr1842_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