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Detailed information for vg0432038119:

Variant ID: vg0432038119 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32038119
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


ACATGAATGCTCAAAACCCAAAAGAGTACCATCTTGTTCTCTTGGTGTGATCAAATAAATACAAAAAAAAGAGAAGTGCATTCGAATTCATTACCCAACT[T/C]
GGCGTGCTGGGCATTCTCTGCATCCATCGTACTACGGAGCTTCTCCTGCTCGACCAAGTAGCCGTCCTCCAACTCAATGTACCAGCGGATGCAAGCTCTC

Reverse complement sequence

GAGAGCTTGCATCCGCTGGTACATTGAGTTGGAGGACGGCTACTTGGTCGAGCAGGAGAAGCTCCGTAGTACGATGGATGCAGAGAATGCCCAGCACGCC[A/G]
AGTTGGGTAATGAATTCGAATGCACTTCTCTTTTTTTTGTATTTATTTGATCACACCAAGAGAACAAGATGGTACTCTTTTGGGTTTTGAGCATTCATGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.60% 44.20% 0.08% 0.08% NA
All Indica  2759 31.80% 68.00% 0.14% 0.07% NA
All Japonica  1512 95.40% 4.60% 0.00% 0.07% NA
Aus  269 71.70% 28.30% 0.00% 0.00% NA
Indica I  595 17.10% 82.70% 0.17% 0.00% NA
Indica II  465 64.10% 35.90% 0.00% 0.00% NA
Indica III  913 17.60% 82.00% 0.11% 0.22% NA
Indica Intermediate  786 40.10% 59.70% 0.25% 0.00% NA
Temperate Japonica  767 95.70% 4.30% 0.00% 0.00% NA
Tropical Japonica  504 94.40% 5.40% 0.00% 0.20% NA
Japonica Intermediate  241 96.30% 3.70% 0.00% 0.00% NA
VI/Aromatic  96 58.30% 41.70% 0.00% 0.00% NA
Intermediate  90 67.80% 31.10% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0432038119 T -> C LOC_Os04g53760.1 missense_variant ; p.Lys137Glu; MODERATE nonsynonymous_codon ; K137E Average:71.008; most accessible tissue: Minghui63 flower, score: 81.266 benign -0.917 TOLERATED 1.00
vg0432038119 T -> C LOC_Os04g53760.2 missense_variant ; p.Lys137Glu; MODERATE nonsynonymous_codon ; K137E Average:71.008; most accessible tissue: Minghui63 flower, score: 81.266 benign -0.917 TOLERATED 1.00
vg0432038119 T -> DEL LOC_Os04g53760.2 N frameshift_variant Average:71.008; most accessible tissue: Minghui63 flower, score: 81.266 N N N N
vg0432038119 T -> DEL LOC_Os04g53760.1 N frameshift_variant Average:71.008; most accessible tissue: Minghui63 flower, score: 81.266 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432038119 1.17E-06 1.83E-08 mr1359_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