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Detailed information for vg0105335997:

Variant ID: vg0105335997 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5335997
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAACCCTTGGCCCTGTTCCTTTCTCCAACAAAAGTCGGATAAAATTTTAAATACTCGTGTCACATTTTTCAAACCGCTAAATGATATGTTTCATGCGAAA[T/A]
CTTTATATACGAAATTTGCTTTAAAATATCATATTAATCTATTTTTCAAGTTTGTAATAATTAAAACTCAATTAACTATACATTAATATCACCTTATTTT

Reverse complement sequence

AAAATAAGGTGATATTAATGTATAGTTAATTGAGTTTTAATTATTACAAACTTGAAAAATAGATTAATATGATATTTTAAAGCAAATTTCGTATATAAAG[A/T]
TTTCGCATGAAACATATCATTTAGCGGTTTGAAAAATGTGACACGAGTATTTAAAATTTTATCCGACTTTTGTTGGAGAAAGGAACAGGGCCAAGGGTTA

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 65.20% 34.70% 0.06% 0.00% NA
All Indica  2759 98.90% 1.00% 0.07% 0.00% NA
All Japonica  1512 1.90% 98.10% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 98.70% 1.10% 0.22% 0.00% NA
Indica III  913 98.90% 1.00% 0.11% 0.00% NA
Indica Intermediate  786 98.60% 1.40% 0.00% 0.00% NA
Temperate Japonica  767 1.40% 98.60% 0.00% 0.00% NA
Tropical Japonica  504 3.20% 96.80% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 54.40% 44.40% 1.11% 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
vg0105335997 T -> A LOC_Os01g10150.1 upstream_gene_variant ; 479.0bp to feature; MODIFIER silent_mutation Average:51.1; most accessible tissue: Callus, score: 65.882 N N N N
vg0105335997 T -> A LOC_Os01g10170.1 upstream_gene_variant ; 3447.0bp to feature; MODIFIER silent_mutation Average:51.1; most accessible tissue: Callus, score: 65.882 N N N N
vg0105335997 T -> A LOC_Os01g10150.2 upstream_gene_variant ; 479.0bp to feature; MODIFIER silent_mutation Average:51.1; most accessible tissue: Callus, score: 65.882 N N N N
vg0105335997 T -> A LOC_Os01g10160.1 downstream_gene_variant ; 707.0bp to feature; MODIFIER silent_mutation Average:51.1; most accessible tissue: Callus, score: 65.882 N N N N
vg0105335997 T -> A LOC_Os01g10150-LOC_Os01g10160 intergenic_region ; MODIFIER silent_mutation Average:51.1; most accessible tissue: Callus, score: 65.882 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105335997 NA 1.48E-06 mr1574 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
vg0105335997 NA 4.89E-07 mr1781 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
vg0105335997 NA 1.31E-06 mr1568_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
vg0105335997 2.64E-06 NA mr1769_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