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Detailed information for vg0516758193:

Variant ID: vg0516758193 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 16758193
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCAAGGTGGATGTTTGTTTGTCCTTGTCAGCAAACAGAAGGGGGCAAAAGGCGGCCAAAGTGCAACAATATTCTAAACATGGTGCAAACCATAGACTTT[T/C]
CTTAAACATGGTGCAAGCTGCAAGAAGCACCCTAAGTCCTGGTTCAAACTGTAATTCTTGCTCTTCTTTTATTTGTCAAGTGCAGTCTGGAAAGCAGTGC

Reverse complement sequence

GCACTGCTTTCCAGACTGCACTTGACAAATAAAAGAAGAGCAAGAATTACAGTTTGAACCAGGACTTAGGGTGCTTCTTGCAGCTTGCACCATGTTTAAG[A/G]
AAAGTCTATGGTTTGCACCATGTTTAGAATATTGTTGCACTTTGGCCGCCTTTTGCCCCCTTCTGTTTGCTGACAAGGACAAACAAACATCCACCTTGCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.40% 3.20% 0.40% 0.00% NA
All Indica  2759 95.90% 3.70% 0.36% 0.00% NA
All Japonica  1512 96.40% 3.10% 0.53% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 78.70% 19.40% 1.94% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.50% 0.13% 0.00% NA
Temperate Japonica  767 99.20% 0.50% 0.26% 0.00% NA
Tropical Japonica  504 91.70% 7.10% 1.19% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 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
vg0516758193 T -> C LOC_Os05g28610-LOC_Os05g28630 intergenic_region ; MODIFIER silent_mutation Average:58.034; most accessible tissue: Callus, score: 79.272 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0516758193 NA 2.56E-09 mr1039 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
vg0516758193 NA 9.15E-09 mr1044 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
vg0516758193 NA 3.95E-06 mr1069 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
vg0516758193 NA 7.47E-06 mr1077 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
vg0516758193 NA 3.68E-06 mr1082 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
vg0516758193 NA 2.55E-06 mr1103 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
vg0516758193 NA 2.62E-08 mr1482 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
vg0516758193 NA 1.21E-06 mr1632 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
vg0516758193 NA 1.54E-07 mr1726 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
vg0516758193 NA 1.62E-09 mr1039_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