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Detailed information for vg0804590579:

Variant ID: vg0804590579 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 4590579
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


AAGCTGTTTGTTACGGTCTCTTTTTTTATCTTATTGAATAGACCCAGCAGAATGTCCATTATCCAATTTCAAGCAAGATATATTTTTCTCTACCCTAATA[T/C]
TCAAAACCAGAGGGTTGTGTCTGCAAACGATTGGGTGGACCTGGTTTTATAATAGGGGGGAAGGCTGCGCAAGGGAATAGAAACTTGAAACATGTTCACG

Reverse complement sequence

CGTGAACATGTTTCAAGTTTCTATTCCCTTGCGCAGCCTTCCCCCCTATTATAAAACCAGGTCCACCCAATCGTTTGCAGACACAACCCTCTGGTTTTGA[A/G]
TATTAGGGTAGAGAAAAATATATCTTGCTTGAAATTGGATAATGGACATTCTGCTGGGTCTATTCAATAAGATAAAAAAAGAGACCGTAACAAACAGCTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.90% 6.10% 0.02% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 82.10% 17.80% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 87.70% 12.30% 0.00% 0.00% NA
Tropical Japonica  504 89.30% 10.70% 0.00% 0.00% NA
Japonica Intermediate  241 49.40% 50.20% 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
vg0804590579 T -> C LOC_Os08g08090.1 upstream_gene_variant ; 3092.0bp to feature; MODIFIER silent_mutation Average:66.289; most accessible tissue: Minghui63 flower, score: 77.439 N N N N
vg0804590579 T -> C LOC_Os08g08084.1 downstream_gene_variant ; 1420.0bp to feature; MODIFIER silent_mutation Average:66.289; most accessible tissue: Minghui63 flower, score: 77.439 N N N N
vg0804590579 T -> C LOC_Os08g08080.1 intron_variant ; MODIFIER silent_mutation Average:66.289; most accessible tissue: Minghui63 flower, score: 77.439 N N N N
vg0804590579 T -> C LOC_Os08g08080.2 intron_variant ; MODIFIER silent_mutation Average:66.289; most accessible tissue: Minghui63 flower, score: 77.439 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0804590579 NA 6.80E-06 mr1496 Jap_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
vg0804590579 1.06E-06 NA mr1567_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
vg0804590579 1.66E-06 NA mr1588_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
vg0804590579 3.99E-06 NA mr1720_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
vg0804590579 NA 7.59E-06 mr1720_2 Jap_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
vg0804590579 1.33E-07 NA mr1806_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