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Detailed information for vg0518913277:

Variant ID: vg0518913277 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 18913277
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTATAATGTATAACATGTATTCATCCATATATTTTGTAGTAAAACGTGAGGTATCAACTAGTATATACTATTATTGATAGGGCATATTTTGGTAGCAATC[T/C]
AAAACAGCCCGTAAATCTAACTCACGTTGCACCATCTACTACCTCCGTCCCAAAATATAGTAATTTTTAGCTATGAATCTGGATACGCGTTTTTGGACGG

Reverse complement sequence

CCGTCCAAAAACGCGTATCCAGATTCATAGCTAAAAATTACTATATTTTGGGACGGAGGTAGTAGATGGTGCAACGTGAGTTAGATTTACGGGCTGTTTT[A/G]
GATTGCTACCAAAATATGCCCTATCAATAATAGTATATACTAGTTGATACCTCACGTTTTACTACAAAATATATGGATGAATACATGTTATACATTATAG

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 72.30% 27.60% 0.11% 0.00% NA
All Indica  2759 98.60% 1.40% 0.04% 0.00% NA
All Japonica  1512 24.30% 75.70% 0.00% 0.00% NA
Aus  269 98.10% 1.10% 0.74% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.20% 0.13% 0.00% NA
Temperate Japonica  767 12.30% 87.70% 0.00% 0.00% NA
Tropical Japonica  504 36.90% 63.10% 0.00% 0.00% NA
Japonica Intermediate  241 36.10% 63.90% 0.00% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 64.40% 33.30% 2.22% 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
vg0518913277 T -> C LOC_Os05g32410.1 upstream_gene_variant ; 1377.0bp to feature; MODIFIER silent_mutation Average:47.414; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N
vg0518913277 T -> C LOC_Os05g32400.1 downstream_gene_variant ; 3213.0bp to feature; MODIFIER silent_mutation Average:47.414; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N
vg0518913277 T -> C LOC_Os05g32400-LOC_Os05g32410 intergenic_region ; MODIFIER silent_mutation Average:47.414; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0518913277 2.98E-07 NA mr1410 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
vg0518913277 1.36E-07 NA mr1745 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
vg0518913277 5.72E-06 NA mr1301_2 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
vg0518913277 4.36E-08 NA mr1410_2 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