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Detailed information for vg0116398776:

Variant ID: vg0116398776 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 16398776
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTAAAGATAAAGTCTTTAGTCCTAGCCGGAACTAAAGATTTTTGGGATCTTTAGTATCGGTTGGTGAAATCAACTTGGTAATAAAGATAATTTACTTTTT[A/G]
TATGTCTTTTTCCTCCTTCAGCCCGAGCTATTGCTGCCAAAGTAAAGGAACTAGGAGGAAGGGAGGTGCTGCCAAATTTTTTTGTGAAAATATTTTGGTG

Reverse complement sequence

CACCAAAATATTTTCACAAAAAAATTTGGCAGCACCTCCCTTCCTCCTAGTTCCTTTACTTTGGCAGCAATAGCTCGGGCTGAAGGAGGAAAAAGACATA[T/C]
AAAAAGTAAATTATCTTTATTACCAAGTTGATTTCACCAACCGATACTAAAGATCCCAAAAATCTTTAGTTCCGGCTAGGACTAAAGACTTTATCTTTAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.60% 6.30% 0.06% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 81.40% 18.40% 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 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 0.00% 0.00% NA
Temperate Japonica  767 95.80% 4.00% 0.13% 0.00% NA
Tropical Japonica  504 56.50% 43.10% 0.40% 0.00% NA
Japonica Intermediate  241 87.60% 12.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0116398776 A -> G LOC_Os01g29250.1 upstream_gene_variant ; 1011.0bp to feature; MODIFIER silent_mutation Average:32.5; most accessible tissue: Callus, score: 54.55 N N N N
vg0116398776 A -> G LOC_Os01g29260.1 upstream_gene_variant ; 1853.0bp to feature; MODIFIER silent_mutation Average:32.5; most accessible tissue: Callus, score: 54.55 N N N N
vg0116398776 A -> G LOC_Os01g29250-LOC_Os01g29260 intergenic_region ; MODIFIER silent_mutation Average:32.5; most accessible tissue: Callus, score: 54.55 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0116398776 NA 1.34E-07 mr1248 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
vg0116398776 NA 4.85E-06 mr1603 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
vg0116398776 NA 6.92E-09 mr1422_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
vg0116398776 2.66E-06 NA mr1583_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
vg0116398776 NA 3.75E-09 mr1583_2 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
vg0116398776 NA 1.28E-09 mr1705_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
vg0116398776 NA 1.92E-07 mr1705_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