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Detailed information for vg0600160651:

Variant ID: vg0600160651 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 160651
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:


TGTCGCCATTGGTAGGACTGCCATGAGTGTGTGAGAGAGAGAACTTAACTTGAACTATAATTTAATATGTGTGTGAGACTTCTCTTTCCCGGGAGCGCCA[G/A]
AACTCCTCTCACTGCTAGAAACATGGACACCTAGAGTGCATGAGGATTTAAGTTCATGGAGCGGGTACTGCCAATGCGAGGTTATCAAAAAGCTTTGTCG

Reverse complement sequence

CGACAAAGCTTTTTGATAACCTCGCATTGGCAGTACCCGCTCCATGAACTTAAATCCTCATGCACTCTAGGTGTCCATGTTTCTAGCAGTGAGAGGAGTT[C/T]
TGGCGCTCCCGGGAAAGAGAAGTCTCACACACATATTAAATTATAGTTCAAGTTAAGTTCTCTCTCTCACACACTCATGGCAGTCCTACCAATGGCGACA

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 98.20% 1.30% 0.49% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 95.10% 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 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 91.00% 6.30% 2.74% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 98.30% 1.20% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0600160651 G -> A LOC_Os06g01230.1 upstream_gene_variant ; 4033.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0600160651 G -> A LOC_Os06g01250.1 upstream_gene_variant ; 2554.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0600160651 G -> A LOC_Os06g01230.2 upstream_gene_variant ; 4033.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0600160651 G -> A LOC_Os06g01240.1 downstream_gene_variant ; 925.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0600160651 G -> A LOC_Os06g01230-LOC_Os06g01240 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0600160651 2.69E-06 NA mr1218 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
vg0600160651 8.55E-06 8.55E-06 mr1728 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