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Detailed information for vg1216316780:

Variant ID: vg1216316780 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16316780
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGAAGTTACCAACTGGAAGTAATGATTTTTTTTCTTTTTTTTCCTGCTTGCATGATTTCGAGCAACACAAATCATTCATAAAATTATCCACAAATCATTC[G/A]
AACACCACAAATCATTCACAAAATCCCGAAATACATCAAGCTGTATTTTCTTTATATCCCCAAATACATCCACATATCACACATCGCACAGATCAGAAAA

Reverse complement sequence

TTTTCTGATCTGTGCGATGTGTGATATGTGGATGTATTTGGGGATATAAAGAAAATACAGCTTGATGTATTTCGGGATTTTGTGAATGATTTGTGGTGTT[C/T]
GAATGATTTGTGGATAATTTTATGAATGATTTGTGTTGCTCGAAATCATGCAAGCAGGAAAAAAAAGAAAAAAAATCATTACTTCCAGTTGGTAACTTCA

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 88.10% 5.60% 0.11% 6.16% NA
All Indica  2759 95.00% 3.30% 0.11% 1.59% NA
All Japonica  1512 72.90% 11.00% 0.13% 16.01% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 89.70% 2.20% 0.65% 7.53% NA
Indica III  913 94.00% 5.90% 0.00% 0.11% NA
Indica Intermediate  786 95.70% 3.30% 0.00% 1.02% NA
Temperate Japonica  767 98.60% 1.20% 0.00% 0.26% NA
Tropical Japonica  504 28.40% 26.60% 0.20% 44.84% NA
Japonica Intermediate  241 84.20% 9.50% 0.41% 5.81% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 88.90% 5.60% 0.00% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216316780 G -> DEL N N silent_mutation Average:25.038; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N
vg1216316780 G -> A LOC_Os12g27680-LOC_Os12g27690 intergenic_region ; MODIFIER silent_mutation Average:25.038; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216316780 1.55E-06 1.55E-06 mr1266 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
vg1216316780 NA 9.55E-06 mr1408 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
vg1216316780 NA 4.33E-06 mr1518 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
vg1216316780 NA 7.19E-06 mr1682 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
vg1216316780 4.89E-06 NA mr1754 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