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Detailed information for vg1217385743:

Variant ID: vg1217385743 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17385743
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTACTTCCTATTTTTTCCTTTTACGTTTATTTTCATCTGTAATACCCTACAATATATTTATATCACATGATCTGTTTTTTTTATGTTATTGACTTTTC[A/T]
GCGTATATTTAATTATTTGTCTTAGTATAAAAATTATATAATTATAATAGGAAATCCTACAAATTCCAAAAAAAATAAAACATCCAACCCTCGATTTTCA

Reverse complement sequence

TGAAAATCGAGGGTTGGATGTTTTATTTTTTTTGGAATTTGTAGGATTTCCTATTATAATTATATAATTTTTATACTAAGACAAATAATTAAATATACGC[T/A]
GAAAAGTCAATAACATAAAAAAAACAGATCATGTGATATAAATATATTGTAGGGTATTACAGATGAAAATAAACGTAAAAGGAAAAAATAGGAAGTAAAA

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 52.80% 6.70% 3.28% 37.24% NA
All Indica  2759 53.90% 11.20% 5.07% 29.87% NA
All Japonica  1512 59.20% 0.10% 0.26% 40.48% NA
Aus  269 18.20% 0.00% 2.97% 78.81% NA
Indica I  595 62.50% 18.50% 5.71% 13.28% NA
Indica II  465 56.30% 8.80% 3.44% 31.40% NA
Indica III  913 52.00% 6.70% 3.94% 37.35% NA
Indica Intermediate  786 48.00% 12.30% 6.87% 32.82% NA
Temperate Japonica  767 93.50% 0.10% 0.13% 6.26% NA
Tropical Japonica  504 14.10% 0.00% 0.60% 85.32% NA
Japonica Intermediate  241 44.40% 0.00% 0.00% 55.60% NA
VI/Aromatic  96 18.80% 1.00% 1.04% 79.17% NA
Intermediate  90 52.20% 5.60% 2.22% 40.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1217385743 A -> DEL N N silent_mutation Average:35.997; most accessible tissue: Callus, score: 80.342 N N N N
vg1217385743 A -> T LOC_Os12g29320-LOC_Os12g29330 intergenic_region ; MODIFIER silent_mutation Average:35.997; most accessible tissue: Callus, score: 80.342 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217385743 NA 6.78E-06 mr1302_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
vg1217385743 NA 6.65E-06 mr1813_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
vg1217385743 NA 7.31E-06 mr1824_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
vg1217385743 2.83E-06 NA mr1889_2 Ind_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