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Detailed information for vg0527997931:

Variant ID: vg0527997931 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 27997931
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


TAATATACTTAAATACAACGATATCTTGACATAAAGGACAGATTTAACATATCAATGAAGCATATAAAGCAAATATAGTTAAATCAGGTAAGATCGGCTG[A/G]
TACTCCGATACTACTCTATTCGGCAACCAGGAGGCAGGCTAGAGATTGGTATTCTAAGCACGACTTAATAGATCAAACTCAACTGATGCAGTATTAAGTA

Reverse complement sequence

TACTTAATACTGCATCAGTTGAGTTTGATCTATTAAGTCGTGCTTAGAATACCAATCTCTAGCCTGCCTCCTGGTTGCCGAATAGAGTAGTATCGGAGTA[T/C]
CAGCCGATCTTACCTGATTTAACTATATTTGCTTTATATGCTTCATTGATATGTTAAATCTGTCCTTTATGTCAAGATATCGTTGTATTTAAGTATATTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.30% 3.60% 3.17% 0.00% NA
All Indica  2759 88.80% 5.90% 5.29% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.13% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 87.40% 1.50% 11.09% 0.00% NA
Indica II  465 95.10% 1.90% 3.01% 0.00% NA
Indica III  913 88.60% 10.20% 1.20% 0.00% NA
Indica Intermediate  786 86.40% 6.60% 7.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.00% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 5.60% 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
vg0527997931 A -> G LOC_Os05g48840-LOC_Os05g48850 intergenic_region ; MODIFIER silent_mutation Average:33.57; most accessible tissue: Minghui63 young leaf, score: 44.63 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0527997931 1.77E-06 1.77E-06 mr1323 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