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Detailed information for vg0229643363:

Variant ID: vg0229643363 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 29643363
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACATTAAAATACACGGATGGAATAATATTTTGGCCAACTTACCTAAGGTTTGGCTAACAAAATTGAAGATACACTTTAGTTAGCATAAGCCACTATTGCC[A/G]
CATCTTTTTATCTCAATGGCATGCGAAGCCTATATAGTGAAGAAAGAATCTTGTCTTAAGTATGACTAATCCACCTAACTTAGTTAGATTTGTCTAACGC

Reverse complement sequence

GCGTTAGACAAATCTAACTAAGTTAGGTGGATTAGTCATACTTAAGACAAGATTCTTTCTTCACTATATAGGCTTCGCATGCCATTGAGATAAAAAGATG[T/C]
GGCAATAGTGGCTTATGCTAACTAAAGTGTATCTTCAATTTTGTTAGCCAAACCTTAGGTAAGTTGGCCAAAATATTATTCCATCCGTGTATTTTAATGT

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 98.40% 1.10% 0.49% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.00% 3.40% 1.52% 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 91.40% 6.00% 2.61% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 2.50% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0229643363 A -> G LOC_Os02g48410.1 upstream_gene_variant ; 1904.0bp to feature; MODIFIER silent_mutation Average:30.261; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0229643363 A -> G LOC_Os02g48400.1 downstream_gene_variant ; 4012.0bp to feature; MODIFIER silent_mutation Average:30.261; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0229643363 A -> G LOC_Os02g48400-LOC_Os02g48410 intergenic_region ; MODIFIER silent_mutation Average:30.261; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0229643363 NA 9.31E-07 mr1252 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
vg0229643363 3.49E-06 3.49E-06 mr1412 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
vg0229643363 NA 8.18E-06 mr1816 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