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Detailed information for vg1218706273:

Variant ID: vg1218706273 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18706273
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, A: 0.06, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


GGTTTTTCACCGTATCTGCCATGTGGTGCATGGTCATCCACATAAATCTTCCGTTGGACTTCAGTAGCCACTAATTGTGTAAAACACAAAGCTTGGGACA[C/A]
CACAGGGATAGAACATCATCTCTCAGGCCCTCCAATGAGTGCAGGTCAATCGCTTCTCGATTGGCCACAACTATCAATGTGCTCGTTGATGGTATGATTG

Reverse complement sequence

CAATCATACCATCAACGAGCACATTGATAGTTGTGGCCAATCGAGAAGCGATTGACCTGCACTCATTGGAGGGCCTGAGAGATGATGTTCTATCCCTGTG[G/T]
TGTCCCAAGCTTTGTGTTTTACACAATTAGTGGCTACTGAAGTCCAACGGAAGATTTATGTGGATGACCATGCACCACATGGCAGATACGGTGAAAAACC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.20% 37.40% 0.23% 1.16% NA
All Indica  2759 67.10% 30.70% 0.25% 1.99% NA
All Japonica  1512 58.70% 41.10% 0.13% 0.00% NA
Aus  269 16.40% 83.30% 0.37% 0.00% NA
Indica I  595 76.50% 19.30% 0.17% 4.03% NA
Indica II  465 66.00% 33.80% 0.22% 0.00% NA
Indica III  913 66.30% 32.60% 0.00% 1.10% NA
Indica Intermediate  786 61.60% 35.10% 0.64% 2.67% NA
Temperate Japonica  767 39.00% 60.80% 0.26% 0.00% NA
Tropical Japonica  504 93.10% 6.90% 0.00% 0.00% NA
Japonica Intermediate  241 49.80% 50.20% 0.00% 0.00% NA
VI/Aromatic  96 64.60% 35.40% 0.00% 0.00% NA
Intermediate  90 52.20% 46.70% 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
vg1218706273 C -> DEL N N silent_mutation Average:78.771; most accessible tissue: Callus, score: 91.752 N N N N
vg1218706273 C -> A LOC_Os12g31110-LOC_Os12g31120 intergenic_region ; MODIFIER silent_mutation Average:78.771; most accessible tissue: Callus, score: 91.752 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218706273 NA 4.23E-06 mr1397 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
vg1218706273 NA 3.22E-10 mr1457 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
vg1218706273 NA 1.56E-06 mr1457 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
vg1218706273 4.98E-06 NA mr1458 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
vg1218706273 NA 6.08E-14 mr1458 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
vg1218706273 NA 7.10E-06 mr1851 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
vg1218706273 4.72E-06 NA mr1457_2 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
vg1218706273 4.96E-10 NA mr1458_2 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
vg1218706273 NA 1.33E-11 mr1458_2 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
vg1218706273 1.42E-06 4.24E-07 mr1458_2 Jap_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