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Detailed information for vg1202415264:

Variant ID: vg1202415264 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2415264
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


GGACAAGGGGACACCTATAGGTATAAATACAAGCCCCCCTAGGAGGAGAGGGAGGAGGATCAACACCCAACACAATCGACATAGAAGCCACAACATAGAA[G/A]
TCTACATACGCCAAGACATGCCGCCGGATATCGACTTCAGGGATAAGCACGGCTAGTACCCTACGGTGTCTCCGGATACTGTCAGGAGAGACAAAAGCGC

Reverse complement sequence

GCGCTTTTGTCTCTCCTGACAGTATCCGGAGACACCGTAGGGTACTAGCCGTGCTTATCCCTGAAGTCGATATCCGGCGGCATGTCTTGGCGTATGTAGA[C/T]
TTCTATGTTGTGGCTTCTATGTCGATTGTGTTGGGTGTTGATCCTCCTCCCTCTCCTCCTAGGGGGGCTTGTATTTATACCTATAGGTGTCCCCTTGTCC

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 98.30% 1.30% 0.36% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 94.80% 4.10% 1.12% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 94.00% 4.30% 1.69% 0.00% NA
Tropical Japonica  504 99.40% 0.40% 0.20% 0.00% NA
Japonica Intermediate  241 87.60% 11.20% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg1202415264 G -> A LOC_Os12g05360.1 upstream_gene_variant ; 2692.0bp to feature; MODIFIER silent_mutation Average:48.332; most accessible tissue: Minghui63 root, score: 58.187 N N N N
vg1202415264 G -> A LOC_Os12g05350.1 downstream_gene_variant ; 3146.0bp to feature; MODIFIER silent_mutation Average:48.332; most accessible tissue: Minghui63 root, score: 58.187 N N N N
vg1202415264 G -> A LOC_Os12g05350-LOC_Os12g05360 intergenic_region ; MODIFIER silent_mutation Average:48.332; most accessible tissue: Minghui63 root, score: 58.187 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1202415264 4.26E-10 NA mr1549 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
vg1202415264 5.37E-06 NA mr1550 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
vg1202415264 2.28E-08 NA mr1757 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