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Detailed information for vg1117624559:

Variant ID: vg1117624559 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17624559
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTGGCTGTATAGATAAAATAATATTTACATTGTAATATAAAACTACAGTCCTATATAACTAAAATTACATTTGTAAATTCAGTTAATATAACATATAA[G/A,T]
TGCACTATAATTTTGATAAAAATAATCTGTAAGTAAATATGTATTTATTATTTTCTTTTGTAGTCCGTTGGATGTAAATGTAATGGTAGAAAAAATCTGA

Reverse complement sequence

TCAGATTTTTTCTACCATTACATTTACATCCAACGGACTACAAAAGAAAATAATAAATACATATTTACTTACAGATTATTTTTATCAAAATTATAGTGCA[C/T,A]
TTATATGTTATATTAACTGAATTTACAAATGTAATTTTAGTTATATAGGACTGTAGTTTTATATTACAATGTAAATATTATTTTATCTATACAGCCAAAT

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 94.60% 5.20% 0.17% 0.00% T: 0.08%
All Indica  2759 99.50% 0.00% 0.29% 0.00% T: 0.14%
All Japonica  1512 84.10% 15.90% 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 97.80% 0.00% 1.51% 0.00% T: 0.65%
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.10% 0.13% 0.00% T: 0.13%
Temperate Japonica  767 69.40% 30.60% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 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
vg1117624559 G -> T LOC_Os11g30360.1 upstream_gene_variant ; 1229.0bp to feature; MODIFIER silent_mutation Average:41.674; most accessible tissue: Zhenshan97 flower, score: 61.362 N N N N
vg1117624559 G -> T LOC_Os11g30350-LOC_Os11g30360 intergenic_region ; MODIFIER silent_mutation Average:41.674; most accessible tissue: Zhenshan97 flower, score: 61.362 N N N N
vg1117624559 G -> A LOC_Os11g30360.1 upstream_gene_variant ; 1229.0bp to feature; MODIFIER silent_mutation Average:41.674; most accessible tissue: Zhenshan97 flower, score: 61.362 N N N N
vg1117624559 G -> A LOC_Os11g30350-LOC_Os11g30360 intergenic_region ; MODIFIER silent_mutation Average:41.674; most accessible tissue: Zhenshan97 flower, score: 61.362 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117624559 NA 3.38E-11 Heading_date All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1117624559 NA 1.74E-07 mr1354 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
vg1117624559 NA 1.79E-07 mr1829 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
vg1117624559 NA 1.80E-06 mr1829 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
vg1117624559 NA 2.08E-11 mr1902 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
vg1117624559 NA 1.02E-06 mr1902 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
vg1117624559 NA 7.25E-07 mr1321_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
vg1117624559 NA 1.06E-09 mr1354_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
vg1117624559 5.18E-08 NA mr1679_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
vg1117624559 NA 1.50E-06 mr1829_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
vg1117624559 2.06E-06 2.70E-14 mr1902_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
vg1117624559 NA 4.59E-08 mr1902_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