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Detailed information for vg0704728125:

Variant ID: vg0704728125 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 4728125
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATAAAAATTATAATCTTAACTTATACTTTTAGATATTTATACTAAACAGTCAAATAAAATGAATAGTTAAACGTTGTGCTAAAAAGTTAACGATGTCAG[G/A,T]
TACTCCCTCCATCCCATTTTAAATGTAGCCATATATTTTCGTGCTAAACTTTGATCGTTTGTCTTATTTAAAATTTTTTTAAACAATTAAAAAACATAAA

Reverse complement sequence

TTTATGTTTTTTAATTGTTTAAAAAAATTTTAAATAAGACAAACGATCAAAGTTTAGCACGAAAATATATGGCTACATTTAAAATGGGATGGAGGGAGTA[C/T,A]
CTGACATCGTTAACTTTTTAGCACAACGTTTAACTATTCATTTTATTTGACTGTTTAGTATAAATATCTAAAAGTATAAGTTAAGATTATAATTTTTATA

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 91.00% 8.90% 0.04% 0.00% T: 0.08%
All Indica  2759 99.80% 0.10% 0.04% 0.00% T: 0.04%
All Japonica  1512 73.30% 26.70% 0.07% 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 99.20% 0.50% 0.13% 0.00% T: 0.13%
Temperate Japonica  767 97.70% 2.20% 0.13% 0.00% NA
Tropical Japonica  504 45.60% 54.40% 0.00% 0.00% NA
Japonica Intermediate  241 53.50% 46.50% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 13.30% 0.00% 0.00% T: 3.33%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0704728125 G -> A LOC_Os07g09050.1 upstream_gene_variant ; 1341.0bp to feature; MODIFIER silent_mutation Average:28.891; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N
vg0704728125 G -> A LOC_Os07g09050.2 upstream_gene_variant ; 1341.0bp to feature; MODIFIER silent_mutation Average:28.891; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N
vg0704728125 G -> A LOC_Os07g09040.1 downstream_gene_variant ; 1101.0bp to feature; MODIFIER silent_mutation Average:28.891; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N
vg0704728125 G -> A LOC_Os07g09040-LOC_Os07g09050 intergenic_region ; MODIFIER silent_mutation Average:28.891; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N
vg0704728125 G -> T LOC_Os07g09050.1 upstream_gene_variant ; 1341.0bp to feature; MODIFIER silent_mutation Average:28.891; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N
vg0704728125 G -> T LOC_Os07g09050.2 upstream_gene_variant ; 1341.0bp to feature; MODIFIER silent_mutation Average:28.891; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N
vg0704728125 G -> T LOC_Os07g09040.1 downstream_gene_variant ; 1101.0bp to feature; MODIFIER silent_mutation Average:28.891; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N
vg0704728125 G -> T LOC_Os07g09040-LOC_Os07g09050 intergenic_region ; MODIFIER silent_mutation Average:28.891; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0704728125 NA 7.58E-06 mr1509 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
vg0704728125 NA 1.85E-06 mr1363_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
vg0704728125 NA 3.06E-06 mr1509_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
vg0704728125 1.19E-06 NA mr1563_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
vg0704728125 NA 5.10E-07 mr1623_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
vg0704728125 NA 5.61E-07 mr1786_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