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Detailed information for vg0519903067:

Variant ID: vg0519903067 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 19903067
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTAAAAATAAATGTTAAAATCAGTTTAATCTTGTAAAATTCATAACTAATTCATATGAAGTCGGAATGAGGCCGTTCAAGTCTCTAAATTCATCTAAAAT[C/T,A]
ATGATCTACATGTTTGTTTACTTTTTATGTACTATTTATTTGGTTTTTATTAGTCTTTTTCCTCGTTTTGCGTGTTAGCTCGTCGTTTCCGTCGTTTCAA

Reverse complement sequence

TTGAAACGACGGAAACGACGAGCTAACACGCAAAACGAGGAAAAAGACTAATAAAAACCAAATAAATAGTACATAAAAAGTAAACAAACATGTAGATCAT[G/A,T]
ATTTTAGATGAATTTAGAGACTTGAACGGCCTCATTCCGACTTCATATGAATTAGTTATGAATTTTACAAGATTAAACTGATTTTAACATTTATTTTTAG

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 90.30% 0.20% 2.50% 7.00% A: 0.02%
All Indica  2759 96.20% 0.10% 1.38% 2.36% NA
All Japonica  1512 78.00% 0.00% 5.29% 16.60% A: 0.07%
Aus  269 97.00% 1.50% 0.00% 1.49% NA
Indica I  595 97.60% 0.00% 1.34% 1.01% NA
Indica II  465 93.80% 0.00% 4.09% 2.15% NA
Indica III  913 97.30% 0.10% 0.11% 2.52% NA
Indica Intermediate  786 95.20% 0.30% 1.27% 3.31% NA
Temperate Japonica  767 96.90% 0.00% 0.26% 2.87% NA
Tropical Japonica  504 44.60% 0.00% 15.48% 39.88% NA
Japonica Intermediate  241 88.00% 0.00% 0.00% 11.62% A: 0.41%
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 87.80% 0.00% 0.00% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0519903067 C -> T LOC_Os05g33760.1 upstream_gene_variant ; 3235.0bp to feature; MODIFIER silent_mutation Average:13.869; most accessible tissue: Callus, score: 63.176 N N N N
vg0519903067 C -> T LOC_Os05g33780.1 upstream_gene_variant ; 145.0bp to feature; MODIFIER silent_mutation Average:13.869; most accessible tissue: Callus, score: 63.176 N N N N
vg0519903067 C -> T LOC_Os05g33770.1 downstream_gene_variant ; 1962.0bp to feature; MODIFIER silent_mutation Average:13.869; most accessible tissue: Callus, score: 63.176 N N N N
vg0519903067 C -> T LOC_Os05g33780-LOC_Os05g33790 intergenic_region ; MODIFIER silent_mutation Average:13.869; most accessible tissue: Callus, score: 63.176 N N N N
vg0519903067 C -> DEL N N silent_mutation Average:13.869; most accessible tissue: Callus, score: 63.176 N N N N
vg0519903067 C -> A LOC_Os05g33760.1 upstream_gene_variant ; 3235.0bp to feature; MODIFIER silent_mutation Average:13.869; most accessible tissue: Callus, score: 63.176 N N N N
vg0519903067 C -> A LOC_Os05g33780.1 upstream_gene_variant ; 145.0bp to feature; MODIFIER silent_mutation Average:13.869; most accessible tissue: Callus, score: 63.176 N N N N
vg0519903067 C -> A LOC_Os05g33770.1 downstream_gene_variant ; 1962.0bp to feature; MODIFIER silent_mutation Average:13.869; most accessible tissue: Callus, score: 63.176 N N N N
vg0519903067 C -> A LOC_Os05g33780-LOC_Os05g33790 intergenic_region ; MODIFIER silent_mutation Average:13.869; most accessible tissue: Callus, score: 63.176 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0519903067 2.80E-06 5.35E-07 mr1155_2 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
vg0519903067 NA 2.16E-06 mr1277_2 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