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Detailed information for vg1218885208:

Variant ID: vg1218885208 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18885208
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:


GTTTATACTCGAGTATCACAAACCATTTACCTGTATATGGTAATGGTTAAAGTTGCCCTTTGCGGCTATAGTTGCCTCCTGCGCGAGGACTTAAAAATAA[G/A]
AACCACTATACAGAGGTGCCATATTGCTAATTAACATAATAACTAGGTCTGTCTCCATTCTAGAAACTGCGGTCGTACCCGTTCGTTCGACATAAGTACC

Reverse complement sequence

GGTACTTATGTCGAACGAACGGGTACGACCGCAGTTTCTAGAATGGAGACAGACCTAGTTATTATGTTAATTAGCAATATGGCACCTCTGTATAGTGGTT[C/T]
TTATTTTTAAGTCCTCGCGCAGGAGGCAACTATAGCCGCAAAGGGCAACTTTAACCATTACCATATACAGGTAAATGGTTTGTGATACTCGAGTATAAAC

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 96.60% 2.20% 1.16% 0.00% NA
All Indica  2759 99.60% 0.20% 0.22% 0.00% NA
All Japonica  1512 90.30% 6.50% 3.11% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.70% 0.70% 0.67% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.00% 0.25% 0.00% NA
Temperate Japonica  767 93.00% 3.30% 3.78% 0.00% NA
Tropical Japonica  504 84.90% 13.30% 1.79% 0.00% NA
Japonica Intermediate  241 93.40% 2.90% 3.73% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 2.22% 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
vg1218885208 G -> A LOC_Os12g31380.1 upstream_gene_variant ; 2794.0bp to feature; MODIFIER silent_mutation Average:26.969; most accessible tissue: Zhenshan97 root, score: 47.644 N N N N
vg1218885208 G -> A LOC_Os12g31390.1 downstream_gene_variant ; 842.0bp to feature; MODIFIER silent_mutation Average:26.969; most accessible tissue: Zhenshan97 root, score: 47.644 N N N N
vg1218885208 G -> A LOC_Os12g31390-LOC_Os12g31400 intergenic_region ; MODIFIER silent_mutation Average:26.969; most accessible tissue: Zhenshan97 root, score: 47.644 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218885208 NA 3.09E-06 mr1110_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
vg1218885208 NA 3.10E-08 mr1457_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
vg1218885208 NA 1.46E-08 mr1458_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