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Detailed information for vg0601799907:

Variant ID: vg0601799907 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 1799907
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TGCAATCCTTTGTTTTACACTTACATTCCTATCAAAATTTTATTTTCTCTATTCCTAGGTTTTCTCATTCCTGCGATTCAAAGGACCCGGAGAGACGTGT[T/A]
TTCTACTTATCAACGAAGGACGCTGCGACTGATGGTCAAAGAACTCTTGCACGCTGCAGTTTGTAGCATTTTACTCTCGTACTCTTCCATGCCTGCTTCG

Reverse complement sequence

CGAAGCAGGCATGGAAGAGTACGAGAGTAAAATGCTACAAACTGCAGCGTGCAAGAGTTCTTTGACCATCAGTCGCAGCGTCCTTCGTTGATAAGTAGAA[A/T]
ACACGTCTCTCCGGGTCCTTTGAATCGCAGGAATGAGAAAACCTAGGAATAGAGAAAATAAAATTTTGATAGGAATGTAAGTGTAAAACAAAGGATTGCA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.70% 2.00% 0.25% 0.00% NA
All Indica  2759 99.80% 0.10% 0.11% 0.00% NA
All Japonica  1512 93.60% 5.90% 0.53% 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 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.00% 0.25% 0.00% NA
Temperate Japonica  767 99.70% 0.00% 0.26% 0.00% NA
Tropical Japonica  504 81.90% 16.90% 1.19% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 4.40% 1.11% 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
vg0601799907 T -> A LOC_Os06g04250-LOC_Os06g04270 intergenic_region ; MODIFIER silent_mutation Average:57.512; most accessible tissue: Zhenshan97 panicle, score: 81.135 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0601799907 NA 4.16E-06 mr1277 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
vg0601799907 NA 2.97E-06 mr1518 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
vg0601799907 NA 2.69E-06 mr1676 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
vg0601799907 NA 2.47E-07 mr1951 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
vg0601799907 NA 2.47E-06 mr1277_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
vg0601799907 4.87E-06 5.20E-12 mr1993_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