Search for Variation information by Variation ID:

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

Detailed information for vg0107057516:

Variant ID: vg0107057516 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 7057516
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TACACTGTAACTTGCATGTAATTACACTGTAACTATAGTGTAACTTGTATGTAACTTTCAAAAATCTCTTTATAACATGTTATTTTGGTAAAATGGAGGT[C/T]
GTGGGAACAAATTCTTTCACATATGTGTGTGCTATGATTTGTTTTCTTTCTCACCAAAACAAATCTTGTAATAGATCTAACGATTTAAAATTATGTGAAA

Reverse complement sequence

TTTCACATAATTTTAAATCGTTAGATCTATTACAAGATTTGTTTTGGTGAGAAAGAAAACAAATCATAGCACACACATATGTGAAAGAATTTGTTCCCAC[G/A]
ACCTCCATTTTACCAAAATAACATGTTATAAAGAGATTTTTGAAAGTTACATACAAGTTACACTATAGTTACAGTGTAATTACATGCAAGTTACAGTGTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.70% 8.30% 0.02% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 74.90% 25.10% 0.00% 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 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 67.70% 32.30% 0.00% 0.00% NA
Tropical Japonica  504 85.10% 14.90% 0.00% 0.00% NA
Japonica Intermediate  241 76.80% 23.20% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 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
vg0107057516 C -> T LOC_Os01g12760.1 upstream_gene_variant ; 3828.0bp to feature; MODIFIER silent_mutation Average:44.669; most accessible tissue: Callus, score: 68.181 N N N N
vg0107057516 C -> T LOC_Os01g12750.1 downstream_gene_variant ; 1141.0bp to feature; MODIFIER silent_mutation Average:44.669; most accessible tissue: Callus, score: 68.181 N N N N
vg0107057516 C -> T LOC_Os01g12750-LOC_Os01g12760 intergenic_region ; MODIFIER silent_mutation Average:44.669; most accessible tissue: Callus, score: 68.181 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0107057516 NA 3.70E-06 mr1240 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
vg0107057516 NA 2.60E-06 mr1496 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
vg0107057516 1.67E-07 NA mr1679 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
vg0107057516 1.74E-06 2.24E-11 mr1691 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
vg0107057516 NA 1.70E-06 mr1691 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
vg0107057516 NA 2.89E-11 mr1693 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
vg0107057516 9.13E-06 6.74E-08 mr1936 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
vg0107057516 NA 1.19E-07 mr1691_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
vg0107057516 1.18E-06 NA mr1733_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