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Detailed information for vg1221714133:

Variant ID: vg1221714133 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 21714133
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTATTTTTGGCGGGAATCGAGTTGGAGAAGATGCATGGGACCCACGTTTTGGACATGGTTGAGAGAAATGCAGTTTTCTGTTTAGGTTTATTGATATTTC[G/A]
GTTTTTGCTAAAAAAAAACTGGCGATGGATTTTTGTTGGAGAAACTTTCGATTTTCTGGCCGTCAAGATGCGCTTTTTGTTTAGTTACATGCAATGGAAC

Reverse complement sequence

GTTCCATTGCATGTAACTAAACAAAAAGCGCATCTTGACGGCCAGAAAATCGAAAGTTTCTCCAACAAAAATCCATCGCCAGTTTTTTTTTAGCAAAAAC[C/T]
GAAATATCAATAAACCTAAACAGAAAACTGCATTTCTCTCAACCATGTCCAAAACGTGGGTCCCATGCATCTTCTCCAACTCGATTCCCGCCAAAAATAG

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 94.10% 5.70% 0.21% 0.00% NA
All Indica  2759 99.70% 0.10% 0.14% 0.00% NA
All Japonica  1512 82.50% 17.10% 0.40% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 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 99.60% 0.10% 0.25% 0.00% NA
Temperate Japonica  767 78.60% 21.00% 0.39% 0.00% NA
Tropical Japonica  504 97.20% 2.80% 0.00% 0.00% NA
Japonica Intermediate  241 63.90% 34.90% 1.24% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 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
vg1221714133 G -> A LOC_Os12g35710.1 upstream_gene_variant ; 274.0bp to feature; MODIFIER silent_mutation Average:47.38; most accessible tissue: Minghui63 young leaf, score: 72.959 N N N N
vg1221714133 G -> A LOC_Os12g35710-LOC_Os12g35720 intergenic_region ; MODIFIER silent_mutation Average:47.38; most accessible tissue: Minghui63 young leaf, score: 72.959 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1221714133 5.44E-06 1.66E-06 mr1057 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
vg1221714133 5.70E-06 NA mr1092_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
vg1221714133 NA 2.26E-06 mr1781_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
vg1221714133 3.77E-06 NA mr1980_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