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Detailed information for vg0401797247:

Variant ID: vg0401797247 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1797247
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


GAAGTCCGGAGAATCTCTTCGAGATTACATCCGGCAATTTTCTGAACAACGCAACAAGATCTCCGACATCATTGACGATGTTATCATCGCCGCATTCACC[A/G]
AAGGAATTCGCCACGAAGAATTGGTCGGCAAGTTCGGGCGTAAGCATCCCAAAACAGTCAAACTCATGTTTGAAAAAGCCAACGAGTACGCCAAGGCTGA

Reverse complement sequence

TCAGCCTTGGCGTACTCGTTGGCTTTTTCAAACATGAGTTTGACTGTTTTGGGATGCTTACGCCCGAACTTGCCGACCAATTCTTCGTGGCGAATTCCTT[T/C]
GGTGAATGCGGCGATGATAACATCGTCAATGATGTCGGAGATCTTGTTGCGTTGTTCAGAAAATTGCCGGATGTAATCTCGAAGAGATTCTCCGGACTTC

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 76.60% 0.20% 2.26% 20.99% NA
All Indica  2759 77.20% 0.30% 2.32% 20.15% NA
All Japonica  1512 75.40% 0.00% 1.26% 23.35% NA
Aus  269 80.70% 0.00% 2.60% 16.73% NA
Indica I  595 64.20% 0.50% 1.51% 33.78% NA
Indica II  465 70.80% 0.40% 1.29% 27.53% NA
Indica III  913 89.90% 0.10% 3.29% 6.68% NA
Indica Intermediate  786 76.20% 0.30% 2.42% 21.12% NA
Temperate Japonica  767 79.50% 0.00% 0.65% 19.82% NA
Tropical Japonica  504 75.20% 0.00% 0.60% 24.21% NA
Japonica Intermediate  241 62.70% 0.00% 4.56% 32.78% NA
VI/Aromatic  96 64.60% 0.00% 14.58% 20.83% NA
Intermediate  90 76.70% 0.00% 3.33% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0401797247 A -> DEL N N silent_mutation Average:20.138; most accessible tissue: Minghui63 young leaf, score: 43.347 N N N N
vg0401797247 A -> G LOC_Os04g03940.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:20.138; most accessible tissue: Minghui63 young leaf, score: 43.347 N N N N
vg0401797247 A -> G LOC_Os04g03920.1 upstream_gene_variant ; 4276.0bp to feature; MODIFIER silent_mutation Average:20.138; most accessible tissue: Minghui63 young leaf, score: 43.347 N N N N
vg0401797247 A -> G LOC_Os04g03930.1 upstream_gene_variant ; 2264.0bp to feature; MODIFIER silent_mutation Average:20.138; most accessible tissue: Minghui63 young leaf, score: 43.347 N N N N
vg0401797247 A -> G LOC_Os04g03950.1 downstream_gene_variant ; 4748.0bp to feature; MODIFIER silent_mutation Average:20.138; most accessible tissue: Minghui63 young leaf, score: 43.347 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401797247 4.53E-06 4.51E-06 mr1452 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
vg0401797247 NA 1.37E-06 mr1513 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