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Detailed information for vg1105816397:

Variant ID: vg1105816397 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5816397
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTGTAGAAGAAACCTTTTGACAAAATATATATTTTCAAAGCATGGAGCAAATAGTCTGTTTCAATAATTCAGTGAATAATCTAAAAAGAACTAAGCCTAA[G/A]
CATAATTGTCATCTACTGGTATAACCAATTGACCATGTTGCAGGAAGAATGAACCCTGAAAATACATTCAGGCTGAAGATCAAACATTTTACAAATCGAG

Reverse complement sequence

CTCGATTTGTAAAATGTTTGATCTTCAGCCTGAATGTATTTTCAGGGTTCATTCTTCCTGCAACATGGTCAATTGGTTATACCAGTAGATGACAATTATG[C/T]
TTAGGCTTAGTTCTTTTTAGATTATTCACTGAATTATTGAAACAGACTATTTGCTCCATGCTTTGAAAATATATATTTTGTCAAAAGGTTTCTTCTACAG

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 62.10% 4.10% 3.85% 29.92% NA
All Indica  2759 50.20% 0.10% 3.77% 45.99% NA
All Japonica  1512 77.60% 12.50% 4.63% 5.22% NA
Aus  269 95.50% 1.10% 0.74% 2.60% NA
Indica I  595 79.20% 0.00% 3.19% 17.65% NA
Indica II  465 18.10% 0.00% 8.82% 73.12% NA
Indica III  913 45.80% 0.00% 1.20% 53.01% NA
Indica Intermediate  786 52.30% 0.30% 4.20% 43.26% NA
Temperate Japonica  767 63.10% 22.00% 8.60% 6.26% NA
Tropical Japonica  504 95.80% 0.40% 0.20% 3.57% NA
Japonica Intermediate  241 85.90% 7.50% 1.24% 5.39% NA
VI/Aromatic  96 63.50% 0.00% 2.08% 34.38% NA
Intermediate  90 65.60% 1.10% 4.44% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105816397 G -> A LOC_Os11g10600.1 downstream_gene_variant ; 345.0bp to feature; MODIFIER silent_mutation Average:26.549; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg1105816397 G -> A LOC_Os11g10610.1 downstream_gene_variant ; 4436.0bp to feature; MODIFIER silent_mutation Average:26.549; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg1105816397 G -> A LOC_Os11g10600-LOC_Os11g10610 intergenic_region ; MODIFIER silent_mutation Average:26.549; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg1105816397 G -> DEL N N silent_mutation Average:26.549; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105816397 4.13E-06 5.64E-07 mr1045 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
vg1105816397 NA 9.64E-07 mr1397 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
vg1105816397 NA 6.86E-06 mr1576 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