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Detailed information for vg0107026972:

Variant ID: vg0107026972 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 7026972
Reference Allele: AAlternative Allele: G
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: 291. )

Flanking Sequence (100 bp) in Reference Genome:


ATTCTTCTTATTCTTATGTATAGATAAATAACGCTGGCACAAACAAAGGTTTTAGGCCACTGGTAAACTTTTCAGATGAAGATATTTCTCAGGTACGTTA[A/G]
TTATCTTCGGAAAATCAGAGTCTTTTCCATTCTAATAGAGTTCATAGAACTATATTCGTCATGCAACCTGACTTAGTTATTTCATCTTATTTTTCTTTCT

Reverse complement sequence

AGAAAGAAAAATAAGATGAAATAACTAAGTCAGGTTGCATGACGAATATAGTTCTATGAACTCTATTAGAATGGAAAAGACTCTGATTTTCCGAAGATAA[T/C]
TAACGTACCTGAGAAATATCTTCATCTGAAAAGTTTACCAGTGGCCTAAAACCTTTGTTTGTGCCAGCGTTATTTATCTATACATAAGAATAAGAAGAAT

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 83.50% 16.50% 0.06% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 52.20% 47.70% 0.13% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 36.90% 63.10% 0.00% 0.00% NA
Tropical Japonica  504 78.80% 21.20% 0.00% 0.00% NA
Japonica Intermediate  241 45.20% 53.90% 0.83% 0.00% NA
VI/Aromatic  96 69.80% 30.20% 0.00% 0.00% NA
Intermediate  90 78.90% 20.00% 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
vg0107026972 A -> G LOC_Os01g12710.1 intron_variant ; MODIFIER silent_mutation Average:56.978; most accessible tissue: Callus, score: 77.578 N N N N
vg0107026972 A -> G LOC_Os01g12710.2 intron_variant ; MODIFIER silent_mutation Average:56.978; most accessible tissue: Callus, score: 77.578 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0107026972 7.61E-08 NA mr1679 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