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Detailed information for vg0601150840:

Variant ID: vg0601150840 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 1150840
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


AACCCTAACTAAACTATCAACACAACGCTCTGAAAAACGACACAAAAGAGATACCGGGAAGCCTCACGCTCCCCCTCTATTTATACATGAGGTAGGCAGC[C/A]
TAAAGCCACGAACCAAACTCATACTAGAAGCCCTAAACCACCTAGGAAACCTTCTCGTATAAGAAACAAACTTTACATAACCAATCATATCAAATTTGGA

Reverse complement sequence

TCCAAATTTGATATGATTGGTTATGTAAAGTTTGTTTCTTATACGAGAAGGTTTCCTAGGTGGTTTAGGGCTTCTAGTATGAGTTTGGTTCGTGGCTTTA[G/T]
GCTGCCTACCTCATGTATAAATAGAGGGGGAGCGTGAGGCTTCCCGGTATCTCTTTTGTGTCGTTTTTCAGAGCGTTGTGTTGATAGTTTAGTTAGGGTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.70% 0.40% 0.57% 3.30% NA
All Indica  2759 99.90% 0.00% 0.04% 0.04% NA
All Japonica  1512 87.10% 1.30% 1.72% 9.85% 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 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.90% 0.00% 0.00% 0.11% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 94.30% 0.30% 0.52% 4.95% NA
Tropical Japonica  504 80.80% 1.40% 3.17% 14.68% NA
Japonica Intermediate  241 77.60% 4.60% 2.49% 15.35% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 0.00% 0.00% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0601150840 C -> A LOC_Os06g03120.1 upstream_gene_variant ; 2766.0bp to feature; MODIFIER silent_mutation Average:42.231; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0601150840 C -> A LOC_Os06g03110.1 downstream_gene_variant ; 4657.0bp to feature; MODIFIER silent_mutation Average:42.231; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0601150840 C -> A LOC_Os06g03110-LOC_Os06g03120 intergenic_region ; MODIFIER silent_mutation Average:42.231; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0601150840 C -> DEL N N silent_mutation Average:42.231; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0601150840 NA 2.08E-06 mr1101 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
vg0601150840 3.95E-06 1.01E-06 mr1865_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