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Detailed information for vg0424939205:

Variant ID: vg0424939205 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 24939205
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTAATATAATAATAATATTTTTATCGATGGTTATCATTTTTAAAATTTAGTTTTTTTTAATTTCTAACGGTGTGGCATTGAAGTTGACACTAAATAGAT[G/A]
AATTCATGAATATGAAAATTTTTCGACCGTTTCTGCTTGTTTTTTAAAAAATAATAAAATAATGATGCCGTTTCCGACCATTTCCAACCACTTTCATCCC

Reverse complement sequence

GGGATGAAAGTGGTTGGAAATGGTCGGAAACGGCATCATTATTTTATTATTTTTTAAAAAACAAGCAGAAACGGTCGAAAAATTTTCATATTCATGAATT[C/T]
ATCTATTTAGTGTCAACTTCAATGCCACACCGTTAGAAATTAAAAAAAACTAAATTTTAAAAATGATAACCATCGATAAAAATATTATTATTATATTAGT

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 59.40% 3.00% 1.29% 36.35% NA
All Indica  2759 37.10% 0.20% 1.52% 61.22% NA
All Japonica  1512 89.90% 8.60% 0.93% 0.53% NA
Aus  269 98.10% 0.00% 1.49% 0.37% NA
Indica I  595 45.40% 0.00% 1.85% 52.77% NA
Indica II  465 18.30% 0.00% 1.29% 80.43% NA
Indica III  913 34.00% 0.20% 1.53% 64.29% NA
Indica Intermediate  786 45.50% 0.40% 1.40% 52.67% NA
Temperate Japonica  767 99.70% 0.00% 0.13% 0.13% NA
Tropical Japonica  504 71.80% 24.80% 2.18% 1.19% NA
Japonica Intermediate  241 96.70% 2.10% 0.83% 0.41% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 71.10% 6.70% 1.11% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0424939205 G -> DEL N N silent_mutation Average:13.156; most accessible tissue: Callus, score: 76.217 N N N N
vg0424939205 G -> A LOC_Os04g42120.1 upstream_gene_variant ; 423.0bp to feature; MODIFIER silent_mutation Average:13.156; most accessible tissue: Callus, score: 76.217 N N N N
vg0424939205 G -> A LOC_Os04g42130.1 upstream_gene_variant ; 1256.0bp to feature; MODIFIER silent_mutation Average:13.156; most accessible tissue: Callus, score: 76.217 N N N N
vg0424939205 G -> A LOC_Os04g42110.1 downstream_gene_variant ; 3127.0bp to feature; MODIFIER silent_mutation Average:13.156; most accessible tissue: Callus, score: 76.217 N N N N
vg0424939205 G -> A LOC_Os04g42134.1 downstream_gene_variant ; 3916.0bp to feature; MODIFIER silent_mutation Average:13.156; most accessible tissue: Callus, score: 76.217 N N N N
vg0424939205 G -> A LOC_Os04g42120-LOC_Os04g42130 intergenic_region ; MODIFIER silent_mutation Average:13.156; most accessible tissue: Callus, score: 76.217 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0424939205 1.30E-06 NA mr1668 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