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Detailed information for vg0806300284:

Variant ID: vg0806300284 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 6300284
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGATGAATCATACTATATTTATTTATGGTTATATTTAATGGTAGCTCACGATGGTTAATCGTGTTAAGATAATTAATTGATAATTAAAACCTACTTAATG[G/A]
TGGGTTGTGAGCACATGGTTTTGATGGTCGTGCTCATGGCAATTAAGGACTGGTTCGCAAGCTACTATTGTGAAACATTTACCATGCCAACCATAAGTCA

Reverse complement sequence

TGACTTATGGTTGGCATGGTAAATGTTTCACAATAGTAGCTTGCGAACCAGTCCTTAATTGCCATGAGCACGACCATCAAAACCATGTGCTCACAACCCA[C/T]
CATTAAGTAGGTTTTAATTATCAATTAATTATCTTAACACGATTAACCATCGTGAGCTACCATTAAATATAACCATAAATAAATATAGTATGATTCATCC

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 94.50% 5.10% 0.44% 0.00% NA
All Indica  2759 93.30% 6.00% 0.72% 0.00% NA
All Japonica  1512 95.20% 4.80% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 95.90% 3.00% 1.08% 0.00% NA
Indica III  913 87.20% 12.50% 0.33% 0.00% NA
Indica Intermediate  786 95.00% 3.40% 1.53% 0.00% NA
Temperate Japonica  767 90.50% 9.50% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 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
vg0806300284 G -> A LOC_Os08g10700.1 upstream_gene_variant ; 1046.0bp to feature; MODIFIER silent_mutation Average:54.067; most accessible tissue: Minghui63 young leaf, score: 74.007 N N N N
vg0806300284 G -> A LOC_Os08g10690.1 downstream_gene_variant ; 2543.0bp to feature; MODIFIER silent_mutation Average:54.067; most accessible tissue: Minghui63 young leaf, score: 74.007 N N N N
vg0806300284 G -> A LOC_Os08g10700-LOC_Os08g10710 intergenic_region ; MODIFIER silent_mutation Average:54.067; most accessible tissue: Minghui63 young leaf, score: 74.007 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0806300284 3.84E-07 NA mr1193_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