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Detailed information for vg1218105268:

Variant ID: vg1218105268 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18105268
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, T: 0.03, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCGGATACTTTATTTATTAGCAAATAATATATCAAATGATTTAAATAATGGGTCTAGTGGTTCTAGTGTAAGTGCATATTAGTGAGTATAGATTTTAA[A/T]
TTGTTAATTTAATGGGTACACAGTATATAGTATATAATGTTGTAGACTTTATTTTGAAAGAATGCATTATTTGAGAATAATAGTCCAATGTAATAAAAAT

Reverse complement sequence

ATTTTTATTACATTGGACTATTATTCTCAAATAATGCATTCTTTCAAAATAAAGTCTACAACATTATATACTATATACTGTGTACCCATTAAATTAACAA[T/A]
TTAAAATCTATACTCACTAATATGCACTTACACTAGAACCACTAGACCCATTATTTAAATCATTTGATATATTATTTGCTAATAAATAAAGTATCCGAAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.40% 28.40% 2.24% 2.94% NA
All Indica  2759 53.10% 39.00% 2.90% 5.04% NA
All Japonica  1512 87.90% 12.10% 0.00% 0.00% NA
Aus  269 67.30% 24.20% 8.55% 0.00% NA
Indica I  595 17.80% 79.50% 1.01% 1.68% NA
Indica II  465 69.20% 21.30% 3.23% 6.24% NA
Indica III  913 64.30% 23.20% 4.49% 8.00% NA
Indica Intermediate  786 57.10% 37.20% 2.29% 3.44% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 76.20% 23.80% 0.00% 0.00% NA
Japonica Intermediate  241 75.50% 24.50% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 81.10% 15.60% 3.33% 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
vg1218105268 A -> DEL N N silent_mutation Average:10.525; most accessible tissue: Callus, score: 23.16 N N N N
vg1218105268 A -> T LOC_Os12g30160.1 upstream_gene_variant ; 3604.0bp to feature; MODIFIER silent_mutation Average:10.525; most accessible tissue: Callus, score: 23.16 N N N N
vg1218105268 A -> T LOC_Os12g30150.1 downstream_gene_variant ; 3431.0bp to feature; MODIFIER silent_mutation Average:10.525; most accessible tissue: Callus, score: 23.16 N N N N
vg1218105268 A -> T LOC_Os12g30150-LOC_Os12g30160 intergenic_region ; MODIFIER silent_mutation Average:10.525; most accessible tissue: Callus, score: 23.16 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218105268 NA 4.96E-06 mr1139 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
vg1218105268 NA 9.21E-08 mr1155 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
vg1218105268 NA 6.70E-06 mr1170 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
vg1218105268 NA 1.58E-08 mr1227 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
vg1218105268 NA 4.21E-06 mr1227 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
vg1218105268 NA 8.78E-08 mr1272 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
vg1218105268 NA 8.46E-06 mr1291 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
vg1218105268 NA 3.93E-06 mr1335 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
vg1218105268 NA 5.78E-07 mr1364 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
vg1218105268 NA 1.27E-07 mr1443 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
vg1218105268 NA 8.54E-06 mr1502 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
vg1218105268 8.89E-06 8.89E-06 mr1513 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
vg1218105268 5.96E-06 2.03E-06 mr1590 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
vg1218105268 NA 1.38E-10 mr1660 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
vg1218105268 NA 1.03E-06 mr1660 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
vg1218105268 NA 8.33E-06 mr1755 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
vg1218105268 NA 5.60E-06 mr1755 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
vg1218105268 3.70E-06 1.78E-07 mr1884 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
vg1218105268 NA 3.01E-06 mr1958 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
vg1218105268 NA 6.84E-06 mr1958 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