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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0507051194:

Variant ID: vg0507051194 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7051194
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATATTTAACAATGAATCAAATGAGATGAAAAGAATAAATAATTACTTAAATTTTTGAATAAGACGAATGGTCAAACACGACTAAAAAGTCAACGGTGTCA[A/T]
ACATTTTGAAACGGAGGGAGTATTACACAGGCAACACCACACTTATACAGCTTGCGAATGCATCCCCTCTCACATGTTTAAAAAGACGGAAACCAACGGT

Reverse complement sequence

ACCGTTGGTTTCCGTCTTTTTAAACATGTGAGAGGGGATGCATTCGCAAGCTGTATAAGTGTGGTGTTGCCTGTGTAATACTCCCTCCGTTTCAAAATGT[T/A]
TGACACCGTTGACTTTTTAGTCGTGTTTGACCATTCGTCTTATTCAAAAATTTAAGTAATTATTTATTCTTTTCATCTCATTTGATTCATTGTTAAATAT

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 98.90% 0.70% 0.40% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.80% 1.90% 1.26% 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 93.70% 3.80% 2.48% 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 96.70% 3.30% 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
vg0507051194 A -> T LOC_Os05g12280.1 upstream_gene_variant ; 328.0bp to feature; MODIFIER silent_mutation Average:53.458; most accessible tissue: Minghui63 root, score: 68.826 N N N N
vg0507051194 A -> T LOC_Os05g12290.1 upstream_gene_variant ; 4670.0bp to feature; MODIFIER silent_mutation Average:53.458; most accessible tissue: Minghui63 root, score: 68.826 N N N N
vg0507051194 A -> T LOC_Os05g12280-LOC_Os05g12290 intergenic_region ; MODIFIER silent_mutation Average:53.458; most accessible tissue: Minghui63 root, score: 68.826 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507051194 NA 8.58E-07 mr1245 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
vg0507051194 2.60E-06 2.60E-06 mr1373 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
vg0507051194 NA 6.58E-07 mr1648 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
vg0507051194 NA 3.23E-06 mr1697 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
vg0507051194 NA 1.78E-06 mr1510_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