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Detailed information for vg0624474548:

Variant ID: vg0624474548 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 24474548
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCAAAATGCCAAATTGGTAACAATGTTTAGTCCAAAATGAAAAGACTTGCTAATGTCTGGTCCAATTTGCAAATTAGGTAATTAAACCTAGTCCAAAGTG[G/A,T]
AATTCACTCTTAATTTTATTTGTCAGTAGTTAACCTGTTGTGTGTAATACTGCATTTTTATATATAGAGGTGGAGATCAGTATCCCTATGACCCTAATAT

Reverse complement sequence

ATATTAGGGTCATAGGGATACTGATCTCCACCTCTATATATAAAAATGCAGTATTACACACAACAGGTTAACTACTGACAAATAAAATTAAGAGTGAATT[C/T,A]
CACTTTGGACTAGGTTTAATTACCTAATTTGCAAATTGGACCAGACATTAGCAAGTCTTTTCATTTTGGACTAAACATTGTTACCAATTTGGCATTTTGG

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 86.80% 13.10% 0.06% 0.00% NA
All Indica  2759 98.50% 1.50% 0.00% 0.00% NA
All Japonica  1512 68.60% 31.20% 0.20% 0.00% NA
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 98.40% 1.60% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 0.00% 0.00% NA
Temperate Japonica  767 88.50% 11.10% 0.39% 0.00% NA
Tropical Japonica  504 41.50% 58.50% 0.00% 0.00% NA
Japonica Intermediate  241 61.80% 38.20% 0.00% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg0624474548 G -> T LOC_Os06g40980.1 upstream_gene_variant ; 2430.0bp to feature; MODIFIER N Average:64.227; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N
vg0624474548 G -> T LOC_Os06g40980-LOC_Os06g40990 intergenic_region ; MODIFIER N Average:64.227; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N
vg0624474548 G -> A LOC_Os06g40980.1 upstream_gene_variant ; 2430.0bp to feature; MODIFIER silent_mutation Average:64.227; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N
vg0624474548 G -> A LOC_Os06g40980-LOC_Os06g40990 intergenic_region ; MODIFIER silent_mutation Average:64.227; most accessible tissue: Minghui63 panicle, score: 86.85 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0624474548 7.15E-06 NA mr1181_2 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
vg0624474548 NA 1.79E-07 mr1408_2 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
vg0624474548 NA 1.56E-07 mr1794_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