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Detailed information for vg0523191092:

Variant ID: vg0523191092 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 23191092
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


AGAACGCCAGAAACCCTTTTTAGCAACAAGAAATTGCTGTTTGACAACTACAGTTTCGTAGTGCAGGGACTTGAGAACTGGCCGCATCTTTTTTATCATT[T/G]
CTGTGGTGTCTCTCAACACAAACCATCTGTCAGGTCTCAATATCCTGTCTATTTCAGCTGCTACCTCCATGATGTCACACCTAAAATAAAGATGCAAAGA

Reverse complement sequence

TCTTTGCATCTTTATTTTAGGTGTGACATCATGGAGGTAGCAGCTGAAATAGACAGGATATTGAGACCTGACAGATGGTTTGTGTTGAGAGACACCACAG[A/C]
AATGATAAAAAAGATGCGGCCAGTTCTCAAGTCCCTGCACTACGAAACTGTAGTTGTCAAACAGCAATTTCTTGTTGCTAAAAAGGGTTTCTGGCGTTCT

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 81.40% 17.80% 0.13% 0.61% NA
All Indica  2759 69.50% 29.30% 0.18% 1.01% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 96.30% 3.70% 0.00% 0.00% NA
Indica I  595 80.70% 18.20% 0.17% 1.01% NA
Indica II  465 80.20% 18.70% 0.00% 1.08% NA
Indica III  913 56.60% 42.30% 0.22% 0.88% NA
Indica Intermediate  786 69.70% 28.90% 0.25% 1.15% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 73.30% 24.40% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0523191092 T -> DEL LOC_Os05g39520.1 N frameshift_variant Average:67.149; most accessible tissue: Zhenshan97 flower, score: 82.948 N N N N
vg0523191092 T -> G LOC_Os05g39520.1 missense_variant ; p.Glu616Ala; MODERATE nonsynonymous_codon ; E616A Average:67.149; most accessible tissue: Zhenshan97 flower, score: 82.948 benign 0.286 TOLERATED 0.10

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0523191092 NA 5.05E-07 mr1336_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