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Detailed information for vg0922167130:

Variant ID: vg0922167130 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 22167130
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


GGTCGCCCGGCGCGGGGGAGCCGGATCGGGCGCTCCCCCCTCGCACCCCTCCCCCCACGTGTGGGCCCGCCCACTTCTTTCTCATTTTTCCACAAAAGAT[G/A]
TTTCATTCAGTGTATTTATAATGTTTCACTATTTATAGATCTAATGTTGCAGTGAATTAAAATACTTTTTTTAAAAAAAGAAACCCACATATTTTGGAAA

Reverse complement sequence

TTTCCAAAATATGTGGGTTTCTTTTTTTAAAAAAAGTATTTTAATTCACTGCAACATTAGATCTATAAATAGTGAAACATTATAAATACACTGAATGAAA[C/T]
ATCTTTTGTGGAAAAATGAGAAAGAAGTGGGCGGGCCCACACGTGGGGGGAGGGGTGCGAGGGGGGAGCGCCCGATCCGGCTCCCCCGCGCCGGGCGACC

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 77.30% 22.50% 0.17% 0.00% NA
All Indica  2759 61.70% 38.00% 0.29% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 96.70% 3.30% 0.00% 0.00% NA
Indica I  595 63.00% 36.30% 0.67% 0.00% NA
Indica II  465 67.70% 32.00% 0.22% 0.00% NA
Indica III  913 54.70% 45.20% 0.11% 0.00% NA
Indica Intermediate  786 65.40% 34.40% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 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 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
vg0922167130 G -> A LOC_Os09g38520.1 upstream_gene_variant ; 3326.0bp to feature; MODIFIER silent_mutation Average:59.452; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0922167130 G -> A LOC_Os09g38530.1 upstream_gene_variant ; 1316.0bp to feature; MODIFIER silent_mutation Average:59.452; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0922167130 G -> A LOC_Os09g38520-LOC_Os09g38530 intergenic_region ; MODIFIER silent_mutation Average:59.452; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0922167130 NA 3.96E-07 mr1629_2 Ind_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
vg0922167130 NA 1.69E-09 mr1968_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