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Detailed information for vg0418704997:

Variant ID: vg0418704997 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 18704997
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


CATAGGTTATCTATGGTGCACATGTGTCGCAGAGAAAACGAGTATGCACTTTCTGTTAATAGAATTGCAAGCTGTAGCCTTCTTTTCGTGCAAAAACGAA[A/G]
GCAACTTGCTGCATATTTCATCAATTAAAATTTCGTGTTATTTCTTATGAGCTTCCTTTTGCACATGCTTTCAGTAATAGGTTTCTTATGGGCGAATAAC

Reverse complement sequence

GTTATTCGCCCATAAGAAACCTATTACTGAAAGCATGTGCAAAAGGAAGCTCATAAGAAATAACACGAAATTTTAATTGATGAAATATGCAGCAAGTTGC[T/C]
TTCGTTTTTGCACGAAAAGAAGGCTACAGCTTGCAATTCTATTAACAGAAAGTGCATACTCGTTTTCTCTGCGACACATGTGCACCATAGATAACCTATG

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 96.10% 2.40% 1.50% 0.00% NA
All Indica  2759 93.30% 4.10% 2.54% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 81.70% 9.90% 8.40% 0.00% NA
Indica II  465 98.10% 1.70% 0.22% 0.00% NA
Indica III  913 98.40% 1.50% 0.11% 0.00% NA
Indica Intermediate  786 93.50% 4.20% 2.29% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0418704997 A -> G LOC_Os04g31260.1 upstream_gene_variant ; 4263.0bp to feature; MODIFIER silent_mutation Average:40.397; most accessible tissue: Callus, score: 78.671 N N N N
vg0418704997 A -> G LOC_Os04g31270.1 intron_variant ; MODIFIER silent_mutation Average:40.397; most accessible tissue: Callus, score: 78.671 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0418704997 5.87E-06 9.63E-11 mr1038 Ind_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
vg0418704997 1.12E-06 NA mr1141 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
vg0418704997 1.98E-07 2.49E-12 mr1389 Ind_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
vg0418704997 4.72E-08 1.72E-14 mr1038_2 Ind_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
vg0418704997 1.22E-08 1.81E-14 mr1389_2 Ind_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
vg0418704997 NA 1.65E-07 mr1864_2 Ind_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