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Detailed information for vg0505490599:

Variant ID: vg0505490599 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 5490599
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGACGAGGGAGCTCGGGAGTTGGGGAAAACGAAAGAGGACGCCAAGGGGATGCTATATATAGGCTTGGATTGAAGAGATCGGGCTCCAACCGAGAGGAAT[C/T]
GAAGCCGGAAAATCTTCGGGTTAGTTTGGAGAGATAAACTCAAACGGACTCGATTTGGTTTATCCGGGAGAAATTGGTCTCTGAGACTTTAGGGGAAAGG

Reverse complement sequence

CCTTTCCCCTAAAGTCTCAGAGACCAATTTCTCCCGGATAAACCAAATCGAGTCCGTTTGAGTTTATCTCTCCAAACTAACCCGAAGATTTTCCGGCTTC[G/A]
ATTCCTCTCGGTTGGAGCCCGATCTCTTCAATCCAAGCCTATATATAGCATCCCCTTGGCGTCCTCTTTCGTTTTCCCCAACTCCCGAGCTCCCTCGTCA

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 97.60% 2.10% 0.11% 0.19% NA
All Indica  2759 96.00% 3.50% 0.18% 0.33% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 97.40% 2.40% 0.22% 0.00% NA
Indica III  913 94.20% 5.50% 0.00% 0.33% NA
Indica Intermediate  786 94.30% 4.50% 0.51% 0.76% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0505490599 C -> T LOC_Os05g09716.1 upstream_gene_variant ; 768.0bp to feature; MODIFIER silent_mutation Average:64.067; most accessible tissue: Zhenshan97 flag leaf, score: 80.588 N N N N
vg0505490599 C -> T LOC_Os05g09708-LOC_Os05g09716 intergenic_region ; MODIFIER silent_mutation Average:64.067; most accessible tissue: Zhenshan97 flag leaf, score: 80.588 N N N N
vg0505490599 C -> DEL N N silent_mutation Average:64.067; most accessible tissue: Zhenshan97 flag leaf, score: 80.588 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0505490599 8.82E-08 9.05E-10 mr1697 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
vg0505490599 9.63E-08 2.91E-09 mr1697 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