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Detailed information for vg0208428122:

Variant ID: vg0208428122 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8428122
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTAACCTCTTGGAATATTTCCTCTGAGTCTATCTCTCTCATCTGATTCCTGTGTTTTTCCTGTGGTCCAATCAAACGGCTATTCCTTTGTTTTTCCTAT[G/A]
TTTTGTAATCCTCTGTTTTACAATTGTACTCTTGTCAGAATCCTGTGTTTTTTCAATCTATCAGTTTTTTTATTCCTACGATTCAAAGGCGCCCAAAATT

Reverse complement sequence

AATTTTGGGCGCCTTTGAATCGTAGGAATAAAAAAACTGATAGATTGAAAAAACACAGGATTCTGACAAGAGTACAATTGTAAAACAGAGGATTACAAAA[C/T]
ATAGGAAAAACAAAGGAATAGCCGTTTGATTGGACCACAGGAAAAACACAGGAATCAGATGAGAGAGATAGACTCAGAGGAAATATTCCAAGAGGTTAGA

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% 0.42% 0.00% NA
All Indica  2759 99.80% 0.00% 0.22% 0.00% NA
All Japonica  1512 95.20% 3.80% 0.93% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.00% 0.00% 1.01% 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 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 86.70% 10.70% 2.58% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0208428122 G -> A LOC_Os02g15130.1 upstream_gene_variant ; 823.0bp to feature; MODIFIER silent_mutation Average:32.374; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg0208428122 G -> A LOC_Os02g15120.1 downstream_gene_variant ; 4268.0bp to feature; MODIFIER silent_mutation Average:32.374; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg0208428122 G -> A LOC_Os02g15120-LOC_Os02g15130 intergenic_region ; MODIFIER silent_mutation Average:32.374; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208428122 NA 3.48E-06 mr1449_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
vg0208428122 5.48E-07 4.87E-09 mr1623_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
vg0208428122 3.91E-06 NA mr1751_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
vg0208428122 NA 1.50E-06 mr1905_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