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Detailed information for vg0726547690:

Variant ID: vg0726547690 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26547690
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTCTGTTGTTCCATGTATGTTGTGGTGGGTGTCTTCCATGGTGGGTGTGTCCTCTCTCCTCTTAGGGGGTCTTGTATTTATACCCATAGGTGTCCCCTT[G/A]
TCCAAGTAGAACTAGGGAAACCAATATGAATACAATCTAAGTAGTCCTTGTCGTTTCCATGTAAAACTCTGGTTATCTTTTCTTATCCGGAACTCCTCCT

Reverse complement sequence

AGGAGGAGTTCCGGATAAGAAAAGATAACCAGAGTTTTACATGGAAACGACAAGGACTACTTAGATTGTATTCATATTGGTTTCCCTAGTTCTACTTGGA[C/T]
AAGGGGACACCTATGGGTATAAATACAAGACCCCCTAAGAGGAGAGAGGACACACCCACCATGGAAGACACCCACCACAACATACATGGAACAACAGAAG

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 91.90% 8.10% 0.04% 0.00% NA
All Indica  2759 86.50% 13.40% 0.07% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.80% 1.00% 0.17% 0.00% NA
Indica II  465 93.50% 6.50% 0.00% 0.00% NA
Indica III  913 70.40% 29.60% 0.00% 0.00% NA
Indica Intermediate  786 91.60% 8.30% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 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 91.10% 8.90% 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
vg0726547690 G -> A LOC_Os07g44420.1 upstream_gene_variant ; 61.0bp to feature; MODIFIER silent_mutation Average:54.45; most accessible tissue: Zhenshan97 panicle, score: 71.253 N N N N
vg0726547690 G -> A LOC_Os07g44430.1 upstream_gene_variant ; 962.0bp to feature; MODIFIER silent_mutation Average:54.45; most accessible tissue: Zhenshan97 panicle, score: 71.253 N N N N
vg0726547690 G -> A LOC_Os07g44440.1 upstream_gene_variant ; 4091.0bp to feature; MODIFIER silent_mutation Average:54.45; most accessible tissue: Zhenshan97 panicle, score: 71.253 N N N N
vg0726547690 G -> A LOC_Os07g44410.1 downstream_gene_variant ; 2507.0bp to feature; MODIFIER silent_mutation Average:54.45; most accessible tissue: Zhenshan97 panicle, score: 71.253 N N N N
vg0726547690 G -> A LOC_Os07g44420-LOC_Os07g44430 intergenic_region ; MODIFIER silent_mutation Average:54.45; most accessible tissue: Zhenshan97 panicle, score: 71.253 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726547690 NA 1.73E-06 mr1082 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
vg0726547690 NA 3.96E-08 mr1518 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
vg0726547690 NA 2.56E-07 mr1676 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
vg0726547690 NA 1.83E-06 mr1517_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
vg0726547690 NA 1.90E-08 mr1676_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