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Detailed information for vg1222579005:

Variant ID: vg1222579005 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 22579005
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


AAAGAATTTTACTACAAATGTGGTCATGAACTAAATAATAAGCTAACTTAAACTTGTCTAATATATGGCGTGATAGCCTTAGGCAATACTCCATTCGTCC[C/T]
ATAATGTAAGGGATTTTGGGTGGATATAACATATCCTAGTACGATGAATCACATTCACCCAAAATCTCTTATATTATGAGACGAAGGGAGTATTTGACAA

Reverse complement sequence

TTGTCAAATACTCCCTTCGTCTCATAATATAAGAGATTTTGGGTGAATGTGATTCATCGTACTAGGATATGTTATATCCACCCAAAATCCCTTACATTAT[G/A]
GGACGAATGGAGTATTGCCTAAGGCTATCACGCCATATATTAGACAAGTTTAAGTTAGCTTATTATTTAGTTCATGACCACATTTGTAGTAAAATTCTTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.90% 10.00% 0.08% 0.00% NA
All Indica  2759 83.70% 16.20% 0.14% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 95.90% 4.10% 0.00% 0.00% NA
Indica I  595 90.30% 9.70% 0.00% 0.00% NA
Indica II  465 83.70% 16.10% 0.22% 0.00% NA
Indica III  913 80.70% 18.90% 0.33% 0.00% NA
Indica Intermediate  786 82.10% 17.90% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg1222579005 C -> T LOC_Os12g36830.1 upstream_gene_variant ; 1773.0bp to feature; MODIFIER silent_mutation Average:64.246; most accessible tissue: Callus, score: 79.486 N N N N
vg1222579005 C -> T LOC_Os12g36810.1 downstream_gene_variant ; 2716.0bp to feature; MODIFIER silent_mutation Average:64.246; most accessible tissue: Callus, score: 79.486 N N N N
vg1222579005 C -> T LOC_Os12g36820.1 downstream_gene_variant ; 270.0bp to feature; MODIFIER silent_mutation Average:64.246; most accessible tissue: Callus, score: 79.486 N N N N
vg1222579005 C -> T LOC_Os12g36820-LOC_Os12g36830 intergenic_region ; MODIFIER silent_mutation Average:64.246; most accessible tissue: Callus, score: 79.486 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1222579005 NA 8.27E-06 mr1020 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
vg1222579005 1.09E-06 1.72E-07 mr1021 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
vg1222579005 NA 3.16E-06 mr1477 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