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Detailed information for vg1017387324:

Variant ID: vg1017387324 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 17387324
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


AATGGATCAAGAATGGCGTGTCATCGGGCCACGAGTACCCTAAAGCATCTCCAACAGCCTCTCCAATTTTGACTCTCCAAATGTCTATTTGGCCAACTCT[C/T]
AATCTAATTTGGCAAGTCAAACTCTTTACTCCAACAGCCTCTCCATCTATCATCTCCATTACAAGTCAATGATAAATGAAACCCATATGTCAGCCTCATC

Reverse complement sequence

GATGAGGCTGACATATGGGTTTCATTTATCATTGACTTGTAATGGAGATGATAGATGGAGAGGCTGTTGGAGTAAAGAGTTTGACTTGCCAAATTAGATT[G/A]
AGAGTTGGCCAAATAGACATTTGGAGAGTCAAAATTGGAGAGGCTGTTGGAGATGCTTTAGGGTACTCGTGGCCCGATGACACGCCATTCTTGATCCATT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.60% 3.30% 0.51% 12.63% NA
All Indica  2759 72.50% 5.40% 0.87% 21.31% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 82.90% 15.00% 0.00% 2.18% NA
Indica II  465 79.10% 5.20% 1.94% 13.76% NA
Indica III  913 60.60% 0.30% 1.20% 37.90% NA
Indica Intermediate  786 74.40% 4.10% 0.51% 20.99% NA
Temperate Japonica  767 99.50% 0.40% 0.00% 0.13% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 3.30% 0.00% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1017387324 C -> T LOC_Os10g33190.1 downstream_gene_variant ; 2397.0bp to feature; MODIFIER silent_mutation Average:67.347; most accessible tissue: Callus, score: 95.599 N N N N
vg1017387324 C -> T LOC_Os10g33170-LOC_Os10g33190 intergenic_region ; MODIFIER silent_mutation Average:67.347; most accessible tissue: Callus, score: 95.599 N N N N
vg1017387324 C -> DEL N N silent_mutation Average:67.347; most accessible tissue: Callus, score: 95.599 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1017387324 NA 8.09E-06 mr1064 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
vg1017387324 NA 1.54E-06 mr1344 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
vg1017387324 NA 7.41E-06 mr1426 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
vg1017387324 NA 5.91E-06 mr1642 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
vg1017387324 NA 4.88E-07 mr1716 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
vg1017387324 1.54E-06 2.11E-07 mr1745 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
vg1017387324 4.62E-06 4.62E-06 mr1783 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
vg1017387324 8.79E-06 7.53E-07 mr1798 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