Search for Variation information by Variation ID:

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

Detailed information for vg0726691050:

Variant ID: vg0726691050 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26691050
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TTAAGAACTTTATGTTCTGGAAATTATGTCACTTAAAGATTATGATGGGTAAGAAAATCTAAGCATCTGATGAGACACTCTAGAGGAAGCAAACTGCCCT[G/A]
TTGATTTTTATGTGTGAAGGTAGTACATTCCACTTATTGGGTGTCTTTGGATTAGCCACCTATACTCCCTCCTCTTTTTATAGGGCATATTTTATTTTGT

Reverse complement sequence

ACAAAATAAAATATGCCCTATAAAAAGAGGAGGGAGTATAGGTGGCTAATCCAAAGACACCCAATAAGTGGAATGTACTACCTTCACACATAAAAATCAA[C/T]
AGGGCAGTTTGCTTCCTCTAGAGTGTCTCATCAGATGCTTAGATTTTCTTACCCATCATAATCTTTAAGTGACATAATTTCCAGAACATAAAGTTCTTAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.80% 4.10% 0.02% 0.00% NA
All Indica  2759 99.00% 0.90% 0.04% 0.00% NA
All Japonica  1512 89.00% 11.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.10% 3.70% 0.17% 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 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 80.10% 19.90% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 95.00% 5.00% 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
vg0726691050 G -> A LOC_Os07g44710.1 upstream_gene_variant ; 2223.0bp to feature; MODIFIER silent_mutation Average:50.407; most accessible tissue: Callus, score: 89.562 N N N N
vg0726691050 G -> A LOC_Os07g44710-LOC_Os07g44730 intergenic_region ; MODIFIER silent_mutation Average:50.407; most accessible tissue: Callus, score: 89.562 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726691050 2.22E-06 NA mr1922 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
vg0726691050 2.47E-06 7.54E-09 mr1922 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
vg0726691050 NA 8.69E-06 mr1153_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
vg0726691050 NA 9.66E-06 mr1221_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
vg0726691050 2.86E-06 NA mr1252_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
vg0726691050 NA 5.77E-07 mr1383_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