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Detailed information for vg0129128700:

Variant ID: vg0129128700 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 29128700
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGACCCTTAGAGCCAAATGACCGTCTACAAAAATATAAATCGGGGTAAAATTTGATGCCCGCTTGCGAAAATAGATTTTCGCAGACGGACCACTTAAGTG[G/A]
CGCCGCTTAAGTGGTCCGCCTACGAAAATAGACTTGAATATAAATAGACTTGCGGGCCCTATTTTTTTTTTAAGTCCTCACACCTCTCAGTCCTCCCCTC

Reverse complement sequence

GAGGGGAGGACTGAGAGGTGTGAGGACTTAAAAAAAAAATAGGGCCCGCAAGTCTATTTATATTCAAGTCTATTTTCGTAGGCGGACCACTTAAGCGGCG[C/T]
CACTTAAGTGGTCCGTCTGCGAAAATCTATTTTCGCAAGCGGGCATCAAATTTTACCCCGATTTATATTTTTGTAGACGGTCATTTGGCTCTAAGGGTCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.60% 1.40% 0.04% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.90% 4.00% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 95.40% 4.30% 0.26% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 89.60% 10.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 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
vg0129128700 G -> A LOC_Os01g50710.1 upstream_gene_variant ; 2229.0bp to feature; MODIFIER silent_mutation Average:60.723; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg0129128700 G -> A LOC_Os01g50700.1 downstream_gene_variant ; 4064.0bp to feature; MODIFIER silent_mutation Average:60.723; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg0129128700 G -> A LOC_Os01g50720.1 downstream_gene_variant ; 3459.0bp to feature; MODIFIER silent_mutation Average:60.723; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg0129128700 G -> A LOC_Os01g50700-LOC_Os01g50710 intergenic_region ; MODIFIER silent_mutation Average:60.723; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0129128700 NA 1.28E-09 mr1757 Jap_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
vg0129128700 3.56E-07 3.12E-11 mr1549_2 Jap_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
vg0129128700 NA 9.81E-06 mr1550_2 Jap_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
vg0129128700 6.03E-06 9.66E-11 mr1757_2 Jap_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