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Detailed information for vg1218067233:

Variant ID: vg1218067233 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18067233
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCAAAAACTAGTTTATTTCAATAAAATAAATCATGCACAGCCATTTCACGCGACTAATTAGCCAAATTTCCATGCATTGTCATGTACAGACTGCTGAGC[A/G]
CTAAGTTATAATAATTGTAAGGCCATATGGGATACATATATCTACAGGGGTGTTAACATGTGTCATATAACCCAACCTAAAATAGTTATGCAGTTGCAGA

Reverse complement sequence

TCTGCAACTGCATAACTATTTTAGGTTGGGTTATATGACACATGTTAACACCCCTGTAGATATATGTATCCCATATGGCCTTACAATTATTATAACTTAG[T/C]
GCTCAGCAGTCTGTACATGACAATGCATGGAAATTTGGCTAATTAGTCGCGTGAAATGGCTGTGCATGATTTATTTTATTGAAATAAACTAGTTTTTGAA

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 97.90% 2.10% 0.02% 0.00% NA
All Indica  2759 97.30% 2.60% 0.04% 0.00% NA
All Japonica  1512 99.10% 0.90% 0.00% 0.00% NA
Aus  269 96.30% 3.70% 0.00% 0.00% NA
Indica I  595 93.90% 6.10% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 98.80% 1.10% 0.11% 0.00% NA
Indica Intermediate  786 97.10% 2.90% 0.00% 0.00% NA
Temperate Japonica  767 99.20% 0.80% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1218067233 A -> G LOC_Os12g30130.1 upstream_gene_variant ; 1334.0bp to feature; MODIFIER silent_mutation Average:32.29; most accessible tissue: Callus, score: 69.762 N N N N
vg1218067233 A -> G LOC_Os12g30120-LOC_Os12g30130 intergenic_region ; MODIFIER silent_mutation Average:32.29; most accessible tissue: Callus, score: 69.762 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218067233 8.82E-06 6.64E-09 mr1060 Ind_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
vg1218067233 NA 2.32E-06 mr1671 Ind_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
vg1218067233 NA 3.60E-07 mr1937 Ind_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
vg1218067233 NA 4.34E-09 mr1458_2 Ind_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