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Detailed information for vg0517986448:

Variant ID: vg0517986448 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 17986448
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


TTTACCTTGGTCACCTAAATATGGTATTTGGGAAATAAAGTGCATTACTAAGAGAATATATAGTAACATTGATGAACAATTGATTTAACCCATTCCAATT[C/A]
TGTGCCATTCCTAGCTTGTAAAGTTACTACTACTTCTGAATCATGTATTCGTTGTTTTATGCAGACACTGAACTTGGCTCAGCAAGATTTTCTTGGAGAA

Reverse complement sequence

TTCTCCAAGAAAATCTTGCTGAGCCAAGTTCAGTGTCTGCATAAAACAACGAATACATGATTCAGAAGTAGTAGTAACTTTACAAGCTAGGAATGGCACA[G/T]
AATTGGAATGGGTTAAATCAATTGTTCATCAATGTTACTATATATTCTCTTAGTAATGCACTTTATTTCCCAAATACCATATTTAGGTGACCAAGGTAAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.70% 4.90% 2.45% 0.00% NA
All Indica  2759 87.70% 8.30% 3.99% 0.00% NA
All Japonica  1512 99.70% 0.00% 0.26% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 79.70% 11.30% 9.08% 0.00% NA
Indica II  465 93.80% 3.00% 3.23% 0.00% NA
Indica III  913 87.80% 11.70% 0.44% 0.00% NA
Indica Intermediate  786 89.90% 5.30% 4.71% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 99.40% 0.00% 0.60% 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 98.90% 0.00% 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
vg0517986448 C -> A LOC_Os05g30970.1 intron_variant ; MODIFIER silent_mutation Average:53.34; most accessible tissue: Callus, score: 80.699 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0517986448 NA 4.55E-08 mr1038 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
vg0517986448 NA 2.31E-08 mr1389 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
vg0517986448 5.99E-06 3.48E-09 mr1038_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
vg0517986448 NA 1.66E-06 mr1123_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
vg0517986448 1.39E-06 4.90E-07 mr1240_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
vg0517986448 NA 1.07E-07 mr1389_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