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Detailed information for vg0519265938:

Variant ID: vg0519265938 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 19265938
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


GTGTGAGGTCAGTCCGGGCATATGACGCATGGCGCATGTGATCTCTGTGTGAGGCACGTGGCATGGCATATGGCACCAACACTAGACGTATGGATGTGCG[C/T]
TAAGAGGGAGTGAGTTCCTGGGTATTTGCCTATATAAATATGTGGTTATGTGGGTAAATTGAACCGACGACGACCTTGGGTCCTTTGAGCAGGATAGGGG

Reverse complement sequence

CCCCTATCCTGCTCAAAGGACCCAAGGTCGTCGTCGGTTCAATTTACCCACATAACCACATATTTATATAGGCAAATACCCAGGAACTCACTCCCTCTTA[G/A]
CGCACATCCATACGTCTAGTGTTGGTGCCATATGCCATGCCACGTGCCTCACACAGAGATCACATGCGCCATGCGTCATATGCCCGGACTGACCTCACAC

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 98.50% 1.40% 0.17% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.40% 4.10% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 94.00% 5.10% 0.91% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 90.00% 9.50% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 0.00% 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
vg0519265938 C -> T LOC_Os05g32890.1 upstream_gene_variant ; 342.0bp to feature; MODIFIER silent_mutation Average:71.969; most accessible tissue: Zhenshan97 young leaf, score: 87.443 N N N N
vg0519265938 C -> T LOC_Os05g32890-LOC_Os05g32900 intergenic_region ; MODIFIER silent_mutation Average:71.969; most accessible tissue: Zhenshan97 young leaf, score: 87.443 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0519265938 NA 5.02E-06 mr1006 Jap_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
vg0519265938 NA 3.48E-06 mr1007 Jap_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
vg0519265938 NA 9.38E-06 mr1052 Jap_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
vg0519265938 4.16E-06 4.16E-06 mr1130 Jap_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
vg0519265938 NA 2.44E-06 mr1816 Jap_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