Search for Variation information by Variation ID:

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

Detailed information for vg0726883201:

Variant ID: vg0726883201 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26883201
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, T: 0.04, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


TGAATAAATGCATCTCAATAAACTATGATACTTCATATGTCACCAAAAATTTTCACTTGAAAGAATTTTCATTCGAAACCATATGCATAAAAACTGTGCC[A/T]
TATGTACCTAAACACATCAACTCCAATACATAGCAATTGTGACTTAAGTTACTGAAAAATTTTCTCCTTAGCAGACTACCACTGAGTCCTCCCCGCAAAA

Reverse complement sequence

TTTTGCGGGGAGGACTCAGTGGTAGTCTGCTAAGGAGAAAATTTTTCAGTAACTTAAGTCACAATTGCTATGTATTGGAGTTGATGTGTTTAGGTACATA[T/A]
GGCACAGTTTTTATGCATATGGTTTCGAATGAAAATTCTTTCAAGTGAAAATTTTTGGTGACATATGAAGTATCATAGTTTATTGAGATGCATTTATTCA

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 94.70% 5.30% 0.02% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 84.50% 15.40% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 70.50% 29.30% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 3.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0726883201 A -> T LOC_Os07g45050.1 downstream_gene_variant ; 1310.0bp to feature; MODIFIER silent_mutation Average:52.89; most accessible tissue: Callus, score: 86.101 N N N N
vg0726883201 A -> T LOC_Os07g45064.1 downstream_gene_variant ; 3106.0bp to feature; MODIFIER silent_mutation Average:52.89; most accessible tissue: Callus, score: 86.101 N N N N
vg0726883201 A -> T LOC_Os07g45060.1 intron_variant ; MODIFIER silent_mutation Average:52.89; most accessible tissue: Callus, score: 86.101 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726883201 6.54E-07 NA mr1002 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
vg0726883201 NA 2.14E-07 mr1062 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
vg0726883201 NA 8.32E-06 mr1525 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
vg0726883201 NA 7.44E-07 mr1062_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