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Detailed information for vg0819977054:

Variant ID: vg0819977054 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19977054
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, G: 0.10, others allele: 0.00, population size: 51. )

Flanking Sequence (100 bp) in Reference Genome:


TTCCTTTCTGCGGAGGAATCAAAACTAGAGGGGAACTCAAATATTCCTTAATATTATCCAAAGCCTTCTGTTGTTCCGCCCCCCAAGTAAATTGCTGATC[A/G]
GCCTTCAATCTCAATAATGGTGTAAAAGGTTCTAACCTTCCAGACAAGTTAGAAATAAACCTTCGAACAAAATTAATTTTGCCGATCATCTCCTGCAATT

Reverse complement sequence

AATTGCAGGAGATGATCGGCAAAATTAATTTTGTTCGAAGGTTTATTTCTAACTTGTCTGGAAGGTTAGAACCTTTTACACCATTATTGAGATTGAAGGC[T/C]
GATCAGCAATTTACTTGGGGGGCGGAACAACAGAAGGCTTTGGATAATATTAAGGAATATTTGAGTTCCCCTCTAGTTTTGATTCCTCCGCAGAAAGGAA

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 33.80% 0.60% 0.76% 64.79% NA
All Indica  2759 5.00% 1.10% 0.98% 92.93% NA
All Japonica  1512 91.00% 0.00% 0.13% 8.86% NA
Aus  269 1.90% 0.00% 1.12% 97.03% NA
Indica I  595 7.60% 0.00% 0.00% 92.44% NA
Indica II  465 5.20% 3.70% 2.80% 88.39% NA
Indica III  913 2.30% 0.20% 0.44% 97.04% NA
Indica Intermediate  786 6.10% 1.40% 1.27% 91.22% NA
Temperate Japonica  767 99.20% 0.00% 0.00% 0.78% NA
Tropical Japonica  504 79.60% 0.00% 0.40% 20.04% NA
Japonica Intermediate  241 88.80% 0.00% 0.00% 11.20% NA
VI/Aromatic  96 39.60% 0.00% 1.04% 59.38% NA
Intermediate  90 45.60% 0.00% 3.33% 51.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0819977054 A -> G LOC_Os08g32240.1 synonymous_variant ; p.Ala357Ala; LOW synonymous_codon Average:13.613; most accessible tissue: Zhenshan97 panicle, score: 28.447 N N N N
vg0819977054 A -> DEL LOC_Os08g32240.1 N frameshift_variant Average:13.613; most accessible tissue: Zhenshan97 panicle, score: 28.447 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819977054 NA 4.11E-06 mr1184_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
vg0819977054 NA 2.90E-08 mr1449_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
vg0819977054 NA 5.79E-09 mr1690_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
vg0819977054 NA 2.71E-09 mr1851_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
vg0819977054 6.98E-06 NA mr1977_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
vg0819977054 1.78E-06 3.25E-07 mr1977_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
vg0819977054 NA 5.61E-06 mr1992_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