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Detailed information for vg0617714472:

Variant ID: vg0617714472 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 17714472
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


CCTTCAATGTATGACGCACGATATCTCTCTTTATCCATCCATGCCCTGTCCACCATCTATGCATTAATTAATTAATTGCGAAAAAAATAATACAAGTTTA[G/A]
TTAGTTCAAATATTTTGAACAAGATAATTAAAGCTAGCCAAAAATCTGCATATATAAAACATACATCTATCCCTCGGACGAATTACCAAACTACCCTTCT

Reverse complement sequence

AGAAGGGTAGTTTGGTAATTCGTCCGAGGGATAGATGTATGTTTTATATATGCAGATTTTTGGCTAGCTTTAATTATCTTGTTCAAAATATTTGAACTAA[C/T]
TAAACTTGTATTATTTTTTTCGCAATTAATTAATTAATGCATAGATGGTGGACAGGGCATGGATGGATAAAGAGAGATATCGTGCGTCATACATTGAAGG

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 96.20% 0.30% 0.87% 2.64% NA
All Indica  2759 93.60% 0.40% 1.49% 4.46% NA
All Japonica  1512 99.90% 0.00% 0.00% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.00% 0.00% 1.34% 1.68% NA
Indica II  465 92.00% 0.40% 2.15% 5.38% NA
Indica III  913 90.50% 0.40% 1.42% 7.67% NA
Indica Intermediate  786 95.70% 0.80% 1.27% 2.29% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% 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 98.90% 0.00% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0617714472 G -> A LOC_Os06g30610.1 upstream_gene_variant ; 45.0bp to feature; MODIFIER silent_mutation Average:28.223; most accessible tissue: Minghui63 flag leaf, score: 42.036 N N N N
vg0617714472 G -> A LOC_Os06g30620.1 upstream_gene_variant ; 2546.0bp to feature; MODIFIER silent_mutation Average:28.223; most accessible tissue: Minghui63 flag leaf, score: 42.036 N N N N
vg0617714472 G -> A LOC_Os06g30610-LOC_Os06g30620 intergenic_region ; MODIFIER silent_mutation Average:28.223; most accessible tissue: Minghui63 flag leaf, score: 42.036 N N N N
vg0617714472 G -> DEL N N silent_mutation Average:28.223; most accessible tissue: Minghui63 flag leaf, score: 42.036 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0617714472 7.19E-07 2.75E-06 mr1020_2 Ind_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