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Detailed information for vg0826936491:

Variant ID: vg0826936491 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 26936491
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAGGGAGAGAGGGAGGAGGAAGGTCTGTCAGTGGGCCCACATTTCTTTTTGTGTGAATGACTAATGGGTCCCACGCATATTTTTTATTTCTACCGCCAC[G/A]
TAGGTGCCACGTCATCGCCACGTGGAACGAAGACTCGGTCAATATTGCCACGTAGGCGCCACGTGGCACCACGTCAGCAAAACCACCTCCCAAAACCGCC

Reverse complement sequence

GGCGGTTTTGGGAGGTGGTTTTGCTGACGTGGTGCCACGTGGCGCCTACGTGGCAATATTGACCGAGTCTTCGTTCCACGTGGCGATGACGTGGCACCTA[C/T]
GTGGCGGTAGAAATAAAAAATATGCGTGGGACCCATTAGTCATTCACACAAAAAGAAATGTGGGCCCACTGACAGACCTTCCTCCTCCCTCTCTCCCTTC

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 91.20% 5.80% 0.06% 2.90% NA
All Indica  2759 86.70% 8.40% 0.11% 4.86% NA
All Japonica  1512 99.70% 0.10% 0.00% 0.20% NA
Aus  269 86.60% 13.40% 0.00% 0.00% NA
Indica I  595 76.80% 12.90% 0.00% 10.25% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 84.30% 9.30% 0.22% 6.13% NA
Indica Intermediate  786 90.60% 7.10% 0.13% 2.16% NA
Temperate Japonica  767 99.50% 0.30% 0.00% 0.26% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 0.00% 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
vg0826936491 G -> A LOC_Os08g42610.1 upstream_gene_variant ; 1232.0bp to feature; MODIFIER silent_mutation Average:47.179; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0826936491 G -> A LOC_Os08g42620.1 downstream_gene_variant ; 2285.0bp to feature; MODIFIER silent_mutation Average:47.179; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0826936491 G -> A LOC_Os08g42620.2 downstream_gene_variant ; 2285.0bp to feature; MODIFIER silent_mutation Average:47.179; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0826936491 G -> A LOC_Os08g42610-LOC_Os08g42620 intergenic_region ; MODIFIER silent_mutation Average:47.179; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0826936491 G -> DEL N N silent_mutation Average:47.179; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0826936491 2.89E-08 2.93E-08 mr1120 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
vg0826936491 NA 7.78E-06 mr1705 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