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Detailed information for vg0402053743:

Variant ID: vg0402053743 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2053743
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, A: 0.10, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


GTAAATTTGAAATTTTTTAATTACCTAAAATTACATACTGCTAATTAGTCTAAAATCATTCTGCTATGTATATGCAATTTTAGTTTATTTTAAGTGTAGT[C/A]
TTGTTATTGTATTTTGTATTTTTTACCAATTGTAAATTTATTTTGTGTTTAAGTTAGAATAATTCTTTGTTCAATCTTTATCTAATAAAGAAAGGCTTAA

Reverse complement sequence

TTAAGCCTTTCTTTATTAGATAAAGATTGAACAAAGAATTATTCTAACTTAAACACAAAATAAATTTACAATTGGTAAAAAATACAAAATACAATAACAA[G/T]
ACTACACTTAAAATAAACTAAAATTGCATATACATAGCAGAATGATTTTAGACTAATTAGCAGTATGTAATTTTAGGTAATTAAAAAATTTCAAATTTAC

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 83.80% 16.10% 0.06% 0.00% NA
All Indica  2759 75.60% 24.40% 0.07% 0.00% NA
All Japonica  1512 97.20% 2.80% 0.07% 0.00% NA
Aus  269 92.20% 7.80% 0.00% 0.00% NA
Indica I  595 77.00% 23.00% 0.00% 0.00% NA
Indica II  465 95.90% 4.10% 0.00% 0.00% NA
Indica III  913 63.10% 36.80% 0.11% 0.00% NA
Indica Intermediate  786 77.00% 22.90% 0.13% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 93.70% 6.30% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 3.70% 0.00% 0.00% NA
VI/Aromatic  96 80.20% 19.80% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0402053743 C -> A LOC_Os04g04360.1 upstream_gene_variant ; 892.0bp to feature; MODIFIER silent_mutation Average:33.552; most accessible tissue: Callus, score: 64.492 N N N N
vg0402053743 C -> A LOC_Os04g04370.1 downstream_gene_variant ; 3498.0bp to feature; MODIFIER silent_mutation Average:33.552; most accessible tissue: Callus, score: 64.492 N N N N
vg0402053743 C -> A LOC_Os04g04340-LOC_Os04g04360 intergenic_region ; MODIFIER silent_mutation Average:33.552; most accessible tissue: Callus, score: 64.492 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402053743 7.24E-08 NA mr1798_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
vg0402053743 1.06E-08 3.35E-08 mr1798_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