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Detailed information for vg0507074482:

Variant ID: vg0507074482 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7074482
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


GCGCAATTTACTCATTAATAAAATAAGAAGACTTAAATAGAAGAGGTAGAGAGCTGACATACAAAATCTACCATGGGTACAATAAGATTATCGTGAATCA[T/G]
GAAACATATGTGCTTCCATTGTGAATATCTTAAAAGTGCACGATCTTCACAGGAATTCAATGAAAAATTGAGCTAATTCCTATAAAGTCTAGCAAAATAT

Reverse complement sequence

ATATTTTGCTAGACTTTATAGGAATTAGCTCAATTTTTCATTGAATTCCTGTGAAGATCGTGCACTTTTAAGATATTCACAATGGAAGCACATATGTTTC[A/C]
TGATTCACGATAATCTTATTGTACCCATGGTAGATTTTGTATGTCAGCTCTCTACCTCTTCTATTTAAGTCTTCTTATTTTATTAATGAGTAAATTGCGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.60% 8.10% 0.32% 0.00% NA
All Indica  2759 86.20% 13.30% 0.51% 0.00% NA
All Japonica  1512 99.30% 0.60% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 88.10% 11.40% 0.50% 0.00% NA
Indica II  465 76.60% 22.80% 0.65% 0.00% NA
Indica III  913 90.30% 9.60% 0.11% 0.00% NA
Indica Intermediate  786 85.90% 13.20% 0.89% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0507074482 T -> G LOC_Os05g12310.1 downstream_gene_variant ; 2002.0bp to feature; MODIFIER silent_mutation Average:32.252; most accessible tissue: Zhenshan97 flower, score: 51.467 N N N N
vg0507074482 T -> G LOC_Os05g12300-LOC_Os05g12310 intergenic_region ; MODIFIER silent_mutation Average:32.252; most accessible tissue: Zhenshan97 flower, score: 51.467 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507074482 1.80E-13 1.35E-11 mr1593 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
vg0507074482 1.54E-11 5.30E-12 mr1593 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
vg0507074482 4.02E-20 5.70E-15 mr1593_2 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
vg0507074482 1.05E-17 3.38E-17 mr1593_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