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Detailed information for vg1219795565:

Variant ID: vg1219795565 (JBrowse)Variation Type: INDEL
Chromosome: chr12Position: 19795565
Reference Allele: AAlternative Allele: AGAGG
Primary Allele: ASecondary Allele: AGAGG

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


GTAGAGCGGCTTCGGGCCTTGAGCCTTCTTGACATCGTTGAGAGGTGCATGGGAGCATGAGAGGGGGAGTGGGACAACACGTTAGACTAAAGATAGAGAG[A/AGAGG]
GAGAGGGAGAGGGAGAGGAGGAAGATAAGCTGGTGGATGAATCTCAAGATGATGCAAAAGTCCATTTGTAAGATGTTAAGCAACGTTTCCGTTAAATGTG

Reverse complement sequence

CACATTTAACGGAAACGTTGCTTAACATCTTACAAATGGACTTTTGCATCATCTTGAGATTCATCCACCAGCTTATCTTCCTCCTCTCCCTCTCCCTCTC[T/CCTCT]
CTCTCTATCTTTAGTCTAACGTGTTGTCCCACTCCCCCTCTCATGCTCCCATGCACCTCTCAACGATGTCAAGAAGGCTCAAGGCCCGAAGCCGCTCTAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of AGAGG(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.70% 0.50% 0.23% 3.53% NA
All Indica  2759 99.30% 0.70% 0.00% 0.04% NA
All Japonica  1512 88.50% 0.00% 0.66% 10.85% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.90% 0.90% 0.00% 0.22% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.70% 0.00% 0.00% NA
Temperate Japonica  767 82.70% 0.00% 0.65% 16.69% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 83.40% 0.00% 2.07% 14.52% NA
VI/Aromatic  96 97.90% 1.00% 0.00% 1.04% NA
Intermediate  90 96.70% 1.10% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1219795565 A -> DEL N N silent_mutation Average:55.593; most accessible tissue: Callus, score: 75.48 N N N N
vg1219795565 A -> AGAGG LOC_Os12g32760.1 upstream_gene_variant ; 4083.0bp to feature; MODIFIER silent_mutation Average:55.593; most accessible tissue: Callus, score: 75.48 N N N N
vg1219795565 A -> AGAGG LOC_Os12g32770.1 downstream_gene_variant ; 1475.0bp to feature; MODIFIER silent_mutation Average:55.593; most accessible tissue: Callus, score: 75.48 N N N N
vg1219795565 A -> AGAGG LOC_Os12g32770-LOC_Os12g32790 intergenic_region ; MODIFIER silent_mutation Average:55.593; most accessible tissue: Callus, score: 75.48 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1219795565 5.53E-07 5.53E-07 mr1343 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
vg1219795565 NA 2.40E-06 mr1038_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
vg1219795565 NA 2.96E-06 mr1354_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