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Detailed information for vg0528742672:

Variant ID: vg0528742672 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 28742672
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


CCAAACTTCCTTCAAACTTTTAACTTTTCCATCACATCAAAACTTTTCTACACACATAAACTTCTAATTTTTTCGTTACATCGTTCAAATTTCAACCAAA[C/T]
TTCTAATTCATTGTTTTTCTCAACATCCTAGTGACCTTAATTCAGGCCTTTGGCACGATGACTGTGCACCGGTATTGCTGAATAGATGTACTTCCGTCCG

Reverse complement sequence

CGGACGGAAGTACATCTATTCAGCAATACCGGTGCACAGTCATCGTGCCAAAGGCCTGAATTAAGGTCACTAGGATGTTGAGAAAAACAATGAATTAGAA[G/A]
TTTGGTTGAAATTTGAACGATGTAACGAAAAAATTAGAAGTTTATGTGTGTAGAAAAGTTTTGATGTGATGGAAAAGTTAAAAGTTTGAAGGAAGTTTGG

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 93.30% 6.70% 0.00% 0.00% NA
All Indica  2759 95.20% 4.80% 0.00% 0.00% NA
All Japonica  1512 88.30% 11.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 81.90% 18.10% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 95.50% 4.50% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 66.90% 33.10% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 3.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0528742672 C -> T LOC_Os05g50140.1 upstream_gene_variant ; 4743.0bp to feature; MODIFIER silent_mutation Average:56.158; most accessible tissue: Zhenshan97 panicle, score: 85.665 N N N N
vg0528742672 C -> T LOC_Os05g50150.1 upstream_gene_variant ; 3025.0bp to feature; MODIFIER silent_mutation Average:56.158; most accessible tissue: Zhenshan97 panicle, score: 85.665 N N N N
vg0528742672 C -> T LOC_Os05g50140.2 upstream_gene_variant ; 4743.0bp to feature; MODIFIER silent_mutation Average:56.158; most accessible tissue: Zhenshan97 panicle, score: 85.665 N N N N
vg0528742672 C -> T LOC_Os05g50160.1 downstream_gene_variant ; 703.0bp to feature; MODIFIER silent_mutation Average:56.158; most accessible tissue: Zhenshan97 panicle, score: 85.665 N N N N
vg0528742672 C -> T LOC_Os05g50170.1 downstream_gene_variant ; 2617.0bp to feature; MODIFIER silent_mutation Average:56.158; most accessible tissue: Zhenshan97 panicle, score: 85.665 N N N N
vg0528742672 C -> T LOC_Os05g50170.2 downstream_gene_variant ; 4232.0bp to feature; MODIFIER silent_mutation Average:56.158; most accessible tissue: Zhenshan97 panicle, score: 85.665 N N N N
vg0528742672 C -> T LOC_Os05g50150-LOC_Os05g50160 intergenic_region ; MODIFIER silent_mutation Average:56.158; most accessible tissue: Zhenshan97 panicle, score: 85.665 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0528742672 2.09E-06 2.09E-06 mr1173 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