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Detailed information for vg1019739673:

Variant ID: vg1019739673 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 19739673
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 127. )

Flanking Sequence (100 bp) in Reference Genome:


CCTTTCTTGATATCTGATAAATATATTATTAGGCATAAACTCATATCCTTTCCGTGACAACTAAACAGCACTGAAAAGAAAAGTTGTATAAAAATTGATA[A/G]
CATATATCATATCATCATCTATTAGATGTCCATTACAACATCTCTATGTCTACACATTTCACATATAATAAATTACAAAAAAAAACTTAAAAATTTTGAG

Reverse complement sequence

CTCAAAATTTTTAAGTTTTTTTTTGTAATTTATTATATGTGAAATGTGTAGACATAGAGATGTTGTAATGGACATCTAATAGATGATGATATGATATATG[T/C]
TATCAATTTTTATACAACTTTTCTTTTCAGTGCTGTTTAGTTGTCACGGAAAGGATATGAGTTTATGCCTAATAATATATTTATCAGATATCAAGAAAGG

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 87.60% 12.10% 0.32% 0.00% NA
All Indica  2759 91.80% 8.10% 0.07% 0.00% NA
All Japonica  1512 97.90% 1.90% 0.13% 0.00% NA
Aus  269 7.10% 90.70% 2.23% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 78.90% 21.10% 0.00% 0.00% NA
Indica III  913 97.80% 2.10% 0.11% 0.00% NA
Indica Intermediate  786 86.50% 13.50% 0.00% 0.00% NA
Temperate Japonica  767 98.40% 1.40% 0.13% 0.00% NA
Tropical Japonica  504 98.60% 1.20% 0.20% 0.00% NA
Japonica Intermediate  241 95.00% 5.00% 0.00% 0.00% NA
VI/Aromatic  96 33.30% 64.60% 2.08% 0.00% NA
Intermediate  90 80.00% 16.70% 3.33% 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
vg1019739673 A -> G LOC_Os10g36848.1 upstream_gene_variant ; 4632.0bp to feature; MODIFIER silent_mutation Average:23.067; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg1019739673 A -> G LOC_Os10g36848-LOC_Os10g36860 intergenic_region ; MODIFIER silent_mutation Average:23.067; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1019739673 NA 4.62E-13 mr1231 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
vg1019739673 NA 2.94E-09 mr1735 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
vg1019739673 NA 5.52E-06 mr1735_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
vg1019739673 NA 4.38E-06 mr1762_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