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Detailed information for vg1217925281:

Variant ID: vg1217925281 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17925281
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


ACAATGTGCGAATTCCATCTTCCATGATATTAATTATAGGAAAACATTTGGATAAAAAATAACTCATAAACTGATCTTCGTGGTGGATCTGCCACCATCA[C/A]
ATGGCTACTGATATCATAAATATTGACTAGCTTTGCTCACAGGCCAAGCTTATTTGATCAATCCCCCCAGAGTGTCAAACTGAAGGAGACATGAGGAATA

Reverse complement sequence

TATTCCTCATGTCTCCTTCAGTTTGACACTCTGGGGGGATTGATCAAATAAGCTTGGCCTGTGAGCAAAGCTAGTCAATATTTATGATATCAGTAGCCAT[G/T]
TGATGGTGGCAGATCCACCACGAAGATCAGTTTATGAGTTATTTTTTATCCAAATGTTTTCCTATAATTAATATCATGGAAGATGGAATTCGCACATTGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.80% 6.10% 0.04% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 82.00% 18.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 90.70% 9.30% 0.00% 0.00% NA
Tropical Japonica  504 66.90% 33.10% 0.00% 0.00% NA
Japonica Intermediate  241 85.90% 14.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 85.60% 12.20% 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
vg1217925281 C -> A LOC_Os12g29990.1 intron_variant ; MODIFIER silent_mutation Average:64.95; most accessible tissue: Callus, score: 87.203 N N N N
vg1217925281 C -> A LOC_Os12g29990.4 intron_variant ; MODIFIER silent_mutation Average:64.95; most accessible tissue: Callus, score: 87.203 N N N N
vg1217925281 C -> A LOC_Os12g29990.2 intron_variant ; MODIFIER silent_mutation Average:64.95; most accessible tissue: Callus, score: 87.203 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217925281 1.09E-06 NA mr1480 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
vg1217925281 6.04E-06 6.04E-06 mr1480 Jap_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
vg1217925281 NA 7.08E-06 mr1786 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
vg1217925281 NA 5.71E-06 mr1960 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