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Detailed information for vg1214610078:

Variant ID: vg1214610078 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 14610078
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


AGAGGTGCACAACTTAGTGATGGGAATAACCAATGAGTTTGGAAAAAAGAGGAAAGTTGGAAAGACAAAAAAGAAGAGCATGTCGAAGGAAAAAACAGAG[G/A]
AGCATGTGGAAAAACAAAAGACAAAAGAGAGGAGCATGTGGAAAAAGAAGTCAATATTTTGGAGACTACCATACTAGAAGGATCTTAAAGTTCGCCACTG

Reverse complement sequence

CAGTGGCGAACTTTAAGATCCTTCTAGTATGGTAGTCTCCAAAATATTGACTTCTTTTTCCACATGCTCCTCTCTTTTGTCTTTTGTTTTTCCACATGCT[C/T]
CTCTGTTTTTTCCTTCGACATGCTCTTCTTTTTTGTCTTTCCAACTTTCCTCTTTTTTCCAAACTCATTGGTTATTCCCATCACTAAGTTGTGCACCTCT

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 55.00% 3.00% 24.71% 17.27% NA
All Indica  2759 41.00% 2.60% 30.59% 25.81% NA
All Japonica  1512 71.40% 4.20% 18.65% 5.82% NA
Aus  269 93.70% 0.70% 4.09% 1.49% NA
Indica I  595 44.70% 1.50% 31.43% 22.35% NA
Indica II  465 34.40% 3.70% 35.91% 26.02% NA
Indica III  913 41.50% 3.40% 25.41% 29.68% NA
Indica Intermediate  786 41.30% 2.00% 32.82% 23.79% NA
Temperate Japonica  767 90.00% 1.00% 8.08% 0.91% NA
Tropical Japonica  504 45.00% 9.30% 31.94% 13.69% NA
Japonica Intermediate  241 67.20% 3.30% 24.48% 4.98% NA
VI/Aromatic  96 83.30% 0.00% 9.38% 7.29% NA
Intermediate  90 65.60% 4.40% 24.44% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1214610078 G -> DEL N N silent_mutation Average:25.068; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg1214610078 G -> A LOC_Os12g25340.1 upstream_gene_variant ; 4946.0bp to feature; MODIFIER silent_mutation Average:25.068; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg1214610078 G -> A LOC_Os12g25330.1 intron_variant ; MODIFIER silent_mutation Average:25.068; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1214610078 NA 1.32E-09 mr1016 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
vg1214610078 NA 2.25E-10 mr1017 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
vg1214610078 NA 2.20E-09 mr1019 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
vg1214610078 NA 1.36E-10 mr1390 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
vg1214610078 NA 3.76E-06 mr1871 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
vg1214610078 NA 7.43E-10 mr1019_2 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
vg1214610078 NA 2.83E-12 mr1055_2 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
vg1214610078 NA 1.45E-14 mr1132_2 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
vg1214610078 NA 1.10E-07 mr1261_2 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
vg1214610078 NA 2.59E-14 mr1390_2 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
vg1214610078 NA 1.53E-14 mr1490_2 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
vg1214610078 5.51E-07 6.23E-08 mr1623_2 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