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Detailed information for vg0137255998:

Variant ID: vg0137255998 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 37255998
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


AATTTGGCAACTTTATCAAAAAAAAATGGTATGGTTGAAAATAGCATCAAAGCGCCTATTCATATTGTGGCCAAAATAAACCTTACTAAGTTTTGGCAAT[G/A]
CCAAAGTTTTAGCAGAATTTCTTATGTATTGACTAAATTTGGCAACAAACTAAACGCGGATAATTTTTTAACAACTTTGTATGGTTAAAAATAGCATCAA

Reverse complement sequence

TTGATGCTATTTTTAACCATACAAAGTTGTTAAAAAATTATCCGCGTTTAGTTTGTTGCCAAATTTAGTCAATACATAAGAAATTCTGCTAAAACTTTGG[C/T]
ATTGCCAAAACTTAGTAAGGTTTATTTTGGCCACAATATGAATAGGCGCTTTGATGCTATTTTCAACCATACCATTTTTTTTTGATAAAGTTGCCAAATT

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 95.60% 2.80% 1.54% 0.00% NA
All Indica  2759 92.70% 4.80% 2.54% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 78.20% 13.60% 8.24% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 92.10% 5.20% 2.67% 0.00% NA
Temperate Japonica  767 99.70% 0.00% 0.26% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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% 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
vg0137255998 G -> A LOC_Os01g64150.1 downstream_gene_variant ; 2140.0bp to feature; MODIFIER silent_mutation Average:51.918; most accessible tissue: Minghui63 panicle, score: 81.412 N N N N
vg0137255998 G -> A LOC_Os01g64140-LOC_Os01g64150 intergenic_region ; MODIFIER silent_mutation Average:51.918; most accessible tissue: Minghui63 panicle, score: 81.412 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0137255998 2.74E-08 1.22E-08 mr1517 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
vg0137255998 2.09E-08 3.92E-07 mr1538 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
vg0137255998 1.31E-07 1.31E-07 mr1778 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