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Detailed information for vg0800728758:

Variant ID: vg0800728758 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 728758
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTTTGTAAAAATTTTCTATAGGAAAGTTGCTTTAAAAAACCATATTAATCCATTTTTAAAATTTAAAATAATTAATACTCAATTAATCATGAGCTAAT[A/G]
GCTCACCTCATTTTACGTATCTTCTCAATCTTCTCAATCCCCTTCTTCTCAAACACACCCTCACTCTCTTTTACTGTTTTTCTCTCGCTTCTTTACCTTT

Reverse complement sequence

AAAGGTAAAGAAGCGAGAGAAAAACAGTAAAAGAGAGTGAGGGTGTGTTTGAGAAGAAGGGGATTGAGAAGATTGAGAAGATACGTAAAATGAGGTGAGC[T/C]
ATTAGCTCATGATTAATTGAGTATTAATTATTTTAAATTTTAAAAATGGATTAATATGGTTTTTTAAAGCAACTTTCCTATAGAAAATTTTTACAAAAAA

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 60.80% 39.10% 0.04% 0.00% NA
All Indica  2759 90.60% 9.30% 0.07% 0.00% NA
All Japonica  1512 3.70% 96.30% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 90.90% 8.90% 0.17% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 88.70% 11.30% 0.00% 0.00% NA
Indica Intermediate  786 88.50% 11.30% 0.13% 0.00% NA
Temperate Japonica  767 1.60% 98.40% 0.00% 0.00% NA
Tropical Japonica  504 7.70% 92.30% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 48.90% 51.10% 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
vg0800728758 A -> G LOC_Os08g02160.1 upstream_gene_variant ; 3265.0bp to feature; MODIFIER silent_mutation Average:44.221; most accessible tissue: Callus, score: 60.707 N N N N
vg0800728758 A -> G LOC_Os08g02150-LOC_Os08g02160 intergenic_region ; MODIFIER silent_mutation Average:44.221; most accessible tissue: Callus, score: 60.707 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0800728758 NA 2.21E-07 mr1659 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
vg0800728758 NA 6.44E-07 mr1785 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
vg0800728758 NA 4.55E-11 mr1216_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
vg0800728758 NA 3.00E-06 mr1836_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