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Detailed information for vg0125070140:

Variant ID: vg0125070140 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 25070140
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.76, A: 0.23, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


TTTAAAATATTTATATAAATATAATAAAAGGAAAAGTTACGTTTAAAATAAGTAAGTTGCAAATAAAATAAATAATAATTTTAAAATTTTTTAATAAGAT[A/G]
AATGGTCAAATAGTGCAATTAAAATGTCCCTATAAAGAGGGAGGGAGTACTACCTACCAATGCTAGCAACTCGGATCGGCTTGAACAGATCAACACAAGT

Reverse complement sequence

ACTTGTGTTGATCTGTTCAAGCCGATCCGAGTTGCTAGCATTGGTAGGTAGTACTCCCTCCCTCTTTATAGGGACATTTTAATTGCACTATTTGACCATT[T/C]
ATCTTATTAAAAAATTTTAAAATTATTATTTATTTTATTTGCAACTTACTTATTTTAAACGTAACTTTTCCTTTTATTATATTTATATAAATATTTTAAA

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 86.70% 13.10% 0.21% 0.00% NA
All Indica  2759 85.90% 13.80% 0.25% 0.00% NA
All Japonica  1512 85.30% 14.60% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 78.30% 21.30% 0.34% 0.00% NA
Indica II  465 91.20% 8.40% 0.43% 0.00% NA
Indica III  913 89.00% 11.00% 0.00% 0.00% NA
Indica Intermediate  786 85.00% 14.60% 0.38% 0.00% NA
Temperate Japonica  767 98.00% 1.70% 0.26% 0.00% NA
Tropical Japonica  504 70.60% 29.40% 0.00% 0.00% NA
Japonica Intermediate  241 75.10% 24.90% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 83.30% 15.60% 1.11% 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
vg0125070140 A -> G LOC_Os01g43760.1 upstream_gene_variant ; 576.0bp to feature; MODIFIER silent_mutation Average:63.154; most accessible tissue: Callus, score: 93.607 N N N N
vg0125070140 A -> G LOC_Os01g43774.1 upstream_gene_variant ; 3709.0bp to feature; MODIFIER silent_mutation Average:63.154; most accessible tissue: Callus, score: 93.607 N N N N
vg0125070140 A -> G LOC_Os01g43750.1 downstream_gene_variant ; 1841.0bp to feature; MODIFIER silent_mutation Average:63.154; most accessible tissue: Callus, score: 93.607 N N N N
vg0125070140 A -> G LOC_Os01g43750-LOC_Os01g43760 intergenic_region ; MODIFIER silent_mutation Average:63.154; most accessible tissue: Callus, score: 93.607 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0125070140 4.83E-06 4.83E-06 mr1856 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