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Detailed information for vg0726600658:

Variant ID: vg0726600658 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26600658
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCCTGTCCGGGGATGATTCCGCCGAGTGTGTTATTGATTGTATAAACTGGAAAAAAGAATCATCCCGAGAGGAACCCGGACCCCTCCTTATATAGGGGA[A/T]
GGGATCCGTATTACAGAATACAGTCCATATCCTAACGGAATATGGAATTACAGATAAAATACAATTGTAACCGACTAGGATCCCGGGTATTTTCTTGACA

Reverse complement sequence

TGTCAAGAAAATACCCGGGATCCTAGTCGGTTACAATTGTATTTTATCTGTAATTCCATATTCCGTTAGGATATGGACTGTATTCTGTAATACGGATCCC[T/A]
TCCCCTATATAAGGAGGGGTCCGGGTTCCTCTCGGGATGATTCTTTTTTCCAGTTTATACAATCAATAACACACTCGGCGGAATCATCCCCGGACAGGAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.50% 4.40% 0.13% 0.00% NA
All Indica  2759 99.10% 0.80% 0.18% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 67.30% 32.70% 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 98.70% 0.90% 0.44% 0.00% NA
Indica Intermediate  786 98.20% 1.70% 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 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 13.50% 85.40% 1.04% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0726600658 A -> T LOC_Os07g44540.1 upstream_gene_variant ; 272.0bp to feature; MODIFIER silent_mutation Average:23.774; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 N N N N
vg0726600658 A -> T LOC_Os07g44550.1 upstream_gene_variant ; 2979.0bp to feature; MODIFIER silent_mutation Average:23.774; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 N N N N
vg0726600658 A -> T LOC_Os07g44540-LOC_Os07g44550 intergenic_region ; MODIFIER silent_mutation Average:23.774; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726600658 4.69E-07 NA mr1098 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
vg0726600658 NA 8.76E-10 mr1570 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