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Detailed information for vg0128156866:

Variant ID: vg0128156866 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 28156866
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


ATAGGAAGATGATGACGGCGAGACCATAAGACTCGTAAAGACTAGATGCTATGTTATTGGGGAGAAGCGCTCATAATCAGAGCTTCAGAGATGTAGGCTT[C/T]
GGTTCAATTTCATTAACAAATATCGTGGGCTCCCGTATTGTCTTCTGATGTGTCTTGGGTGATCGATGATTGAAACGATCGGAAAAGTTAGTCATTATTT

Reverse complement sequence

AAATAATGACTAACTTTTCCGATCGTTTCAATCATCGATCACCCAAGACACATCAGAAGACAATACGGGAGCCCACGATATTTGTTAATGAAATTGAACC[G/A]
AAGCCTACATCTCTGAAGCTCTGATTATGAGCGCTTCTCCCCAATAACATAGCATCTAGTCTTTACGAGTCTTATGGTCTCGCCGTCATCATCTTCCTAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.40% 7.30% 0.30% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 79.00% 20.20% 0.73% 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 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 93.60% 5.10% 1.30% 0.00% NA
Tropical Japonica  504 50.00% 50.00% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.20% 0.41% 0.00% NA
VI/Aromatic  96 95.80% 3.10% 1.04% 0.00% NA
Intermediate  90 78.90% 18.90% 2.22% 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
vg0128156866 C -> T LOC_Os01g49010.1 upstream_gene_variant ; 4866.0bp to feature; MODIFIER silent_mutation Average:49.154; most accessible tissue: Minghui63 panicle, score: 78.92 N N N N
vg0128156866 C -> T LOC_Os01g49010.2 upstream_gene_variant ; 4866.0bp to feature; MODIFIER silent_mutation Average:49.154; most accessible tissue: Minghui63 panicle, score: 78.92 N N N N
vg0128156866 C -> T LOC_Os01g49000-LOC_Os01g49010 intergenic_region ; MODIFIER silent_mutation Average:49.154; most accessible tissue: Minghui63 panicle, score: 78.92 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0128156866 4.45E-06 2.90E-06 mr1265 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
vg0128156866 2.24E-06 2.24E-06 mr1265 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
vg0128156866 NA 8.27E-06 mr1528 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