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Detailed information for vg1116467363:

Variant ID: vg1116467363 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 16467363
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTTCGACTATTGGTAGTCGTTTGTTAGTCTCCGGCCACTTGAAGGTAAAAGAAAAAAAAACACCCCATGAAAACGAATTTTCTAGGATTTAACAGTATT[G/A]
TGCTTTCAGTGGTAAGCGACGTACCCGTCGAAACGAGGCGTCTGTGGTGACTTTGTCAATATTAAGGATTTGCCGGCCAATCTTCAAAGATGCTCATAGG

Reverse complement sequence

CCTATGAGCATCTTTGAAGATTGGCCGGCAAATCCTTAATATTGACAAAGTCACCACAGACGCCTCGTTTCGACGGGTACGTCGCTTACCACTGAAAGCA[C/T]
AATACTGTTAAATCCTAGAAAATTCGTTTTCATGGGGTGTTTTTTTTTCTTTTACCTTCAAGTGGCCGGAGACTAACAAACGACTACCAATAGTCGAAGA

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% 0.04% 0.00% NA
All Indica  2759 97.90% 2.00% 0.07% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 51.30% 48.70% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 97.30% 2.70% 0.00% 0.00% NA
Indica Intermediate  786 96.30% 3.40% 0.25% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg1116467363 G -> A LOC_Os11g28550.1 downstream_gene_variant ; 1073.0bp to feature; MODIFIER silent_mutation Average:55.272; most accessible tissue: Zhenshan97 young leaf, score: 75.397 N N N N
vg1116467363 G -> A LOC_Os11g28540-LOC_Os11g28550 intergenic_region ; MODIFIER silent_mutation Average:55.272; most accessible tissue: Zhenshan97 young leaf, score: 75.397 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1116467363 NA 7.36E-07 mr1126_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
vg1116467363 2.67E-06 NA mr1148_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
vg1116467363 7.83E-06 NA mr1263_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