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Detailed information for vg0125352342:

Variant ID: vg0125352342 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 25352342
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAAAAAAGTGAGAAAGAAAAGCACGCGGGAACAGGGGAGGGGGCCAACTGACGCGGGCGCCAGCTAAATTGCTAGCACGTACGTGCGCATTAGCCTCCC[C/A]
AAAGATATGGGTTAATTGGATCATGTTATTGCAAGTTTACCAATTTGCCATTACTATTCACGATATCAGGTTCATGCCACTGAAATTTTGCAAAATTTGA

Reverse complement sequence

TCAAATTTTGCAAAATTTCAGTGGCATGAACCTGATATCGTGAATAGTAATGGCAAATTGGTAAACTTGCAATAACATGATCCAATTAACCCATATCTTT[G/T]
GGGAGGCTAATGCGCACGTACGTGCTAGCAATTTAGCTGGCGCCCGCGTCAGTTGGCCCCCTCCCCTGTTCCCGCGTGCTTTTCTTTCTCACTTTTTTTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.70% 3.30% 0.00% 0.00% NA
All Indica  2759 95.40% 4.60% 0.00% 0.00% NA
All Japonica  1512 98.10% 1.90% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 86.40% 13.60% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 94.50% 5.50% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 95.40% 4.60% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 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
vg0125352342 C -> A LOC_Os01g44210.1 upstream_gene_variant ; 792.0bp to feature; MODIFIER silent_mutation Average:64.767; most accessible tissue: Minghui63 flag leaf, score: 78.154 N N N N
vg0125352342 C -> A LOC_Os01g44220.1 upstream_gene_variant ; 1427.0bp to feature; MODIFIER silent_mutation Average:64.767; most accessible tissue: Minghui63 flag leaf, score: 78.154 N N N N
vg0125352342 C -> A LOC_Os01g44220.2 upstream_gene_variant ; 2454.0bp to feature; MODIFIER silent_mutation Average:64.767; most accessible tissue: Minghui63 flag leaf, score: 78.154 N N N N
vg0125352342 C -> A LOC_Os01g44220.3 upstream_gene_variant ; 2454.0bp to feature; MODIFIER silent_mutation Average:64.767; most accessible tissue: Minghui63 flag leaf, score: 78.154 N N N N
vg0125352342 C -> A LOC_Os01g44220.7 upstream_gene_variant ; 2454.0bp to feature; MODIFIER silent_mutation Average:64.767; most accessible tissue: Minghui63 flag leaf, score: 78.154 N N N N
vg0125352342 C -> A LOC_Os01g44220.6 upstream_gene_variant ; 3884.0bp to feature; MODIFIER silent_mutation Average:64.767; most accessible tissue: Minghui63 flag leaf, score: 78.154 N N N N
vg0125352342 C -> A LOC_Os01g44220.4 upstream_gene_variant ; 3884.0bp to feature; MODIFIER silent_mutation Average:64.767; most accessible tissue: Minghui63 flag leaf, score: 78.154 N N N N
vg0125352342 C -> A LOC_Os01g44220.5 upstream_gene_variant ; 4341.0bp to feature; MODIFIER silent_mutation Average:64.767; most accessible tissue: Minghui63 flag leaf, score: 78.154 N N N N
vg0125352342 C -> A LOC_Os01g44210-LOC_Os01g44220 intergenic_region ; MODIFIER silent_mutation Average:64.767; most accessible tissue: Minghui63 flag leaf, score: 78.154 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0125352342 NA 1.83E-08 mr1533_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
vg0125352342 2.99E-06 2.16E-06 mr1563_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