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Detailed information for vg1125402847:

Variant ID: vg1125402847 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25402847
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCAAATATGGAAACCGAACATGAGCCACAGCAAGTGCAACCCACTCTCTTGGACCTTCATGTCTGGCACCAATATTTCAACTAGGCACCTACAAATTGG[G/A]
CGCAATCGGGCGCTATTTCACCAAGTAGATTGAACATGTTTCACTAAATATATCGAAAATATTTCAGTCTTTTAAAAAGCTGAAACATAATCAAATCACC

Reverse complement sequence

GGTGATTTGATTATGTTTCAGCTTTTTAAAAGACTGAAATATTTTCGATATATTTAGTGAAACATGTTCAATCTACTTGGTGAAATAGCGCCCGATTGCG[C/T]
CCAATTTGTAGGTGCCTAGTTGAAATATTGGTGCCAGACATGAAGGTCCAAGAGAGTGGGTTGCACTTGCTGTGGCTCATGTTCGGTTTCCATATTTGAT

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 93.80% 6.10% 0.06% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 81.30% 18.50% 0.20% 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 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 97.10% 2.90% 0.00% 0.00% NA
Tropical Japonica  504 53.20% 46.40% 0.40% 0.00% NA
Japonica Intermediate  241 90.00% 9.50% 0.41% 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
vg1125402847 G -> A LOC_Os11g42160.1 downstream_gene_variant ; 3543.0bp to feature; MODIFIER silent_mutation Average:30.89; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg1125402847 G -> A LOC_Os11g42170.1 downstream_gene_variant ; 2170.0bp to feature; MODIFIER silent_mutation Average:30.89; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg1125402847 G -> A LOC_Os11g42180.1 downstream_gene_variant ; 3241.0bp to feature; MODIFIER silent_mutation Average:30.89; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg1125402847 G -> A LOC_Os11g42170-LOC_Os11g42180 intergenic_region ; MODIFIER silent_mutation Average:30.89; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125402847 NA 7.45E-06 mr1238 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
vg1125402847 NA 4.85E-07 mr1252 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
vg1125402847 NA 4.40E-06 mr1662 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
vg1125402847 9.98E-08 NA mr1925 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
vg1125402847 NA 8.45E-06 mr1662_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