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Detailed information for vg0427858791:

Variant ID: vg0427858791 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 27858791
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


TAAAGAGCTAAAATTCAAGTTTTTCTTAAAGAACTAGTTTACATATTGCTTGTTATTGACGGTGACTATTTGATCTCCTTTACTATCAATATTAGTTATT[T/C]
GGTCTCACGGTTTATCTTTATCCCACACCCCCTAATCTCAAATCCTGGCTTCGCCCCTGATCCTACCTTACTTCTCACTCACACAAATAAGCATTGTGGG

Reverse complement sequence

CCCACAATGCTTATTTGTGTGAGTGAGAAGTAAGGTAGGATCAGGGGCGAAGCCAGGATTTGAGATTAGGGGGTGTGGGATAAAGATAAACCGTGAGACC[A/G]
AATAACTAATATTGATAGTAAAGGAGATCAAATAGTCACCGTCAATAACAAGCAATATGTAAACTAGTTCTTTAAGAAAAACTTGAATTTTAGCTCTTTA

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 51.70% 48.10% 0.28% 0.00% NA
All Indica  2759 81.40% 18.20% 0.36% 0.00% NA
All Japonica  1512 0.50% 99.50% 0.00% 0.00% NA
Aus  269 58.40% 40.90% 0.74% 0.00% NA
Indica I  595 80.70% 19.20% 0.17% 0.00% NA
Indica II  465 91.80% 7.70% 0.43% 0.00% NA
Indica III  913 78.00% 21.70% 0.33% 0.00% NA
Indica Intermediate  786 79.80% 19.70% 0.51% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 0.60% 99.40% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 34.40% 64.40% 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
vg0427858791 T -> C LOC_Os04g46990.1 upstream_gene_variant ; 3828.0bp to feature; MODIFIER silent_mutation Average:43.716; most accessible tissue: Callus, score: 64.19 N N N N
vg0427858791 T -> C LOC_Os04g47000.1 downstream_gene_variant ; 271.0bp to feature; MODIFIER silent_mutation Average:43.716; most accessible tissue: Callus, score: 64.19 N N N N
vg0427858791 T -> C LOC_Os04g46990-LOC_Os04g47000 intergenic_region ; MODIFIER silent_mutation Average:43.716; most accessible tissue: Callus, score: 64.19 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0427858791 6.88E-07 1.01E-39 mr1873 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
vg0427858791 1.13E-06 2.91E-07 mr1873 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
vg0427858791 NA 9.34E-16 mr1579_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
vg0427858791 8.27E-08 4.04E-39 mr1873_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
vg0427858791 7.71E-07 1.26E-08 mr1873_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