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Detailed information for vg0508103725:

Variant ID: vg0508103725 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 8103725
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: 327. )

Flanking Sequence (100 bp) in Reference Genome:


GTTACCTCACAAAAGAGTAACATTGTAACAAAAAGTTGTCACAGTTGGGATGGTAAGGCCCATTGAGCTGCATCTTTCAAAGCATTTGACCACTCTTGGT[C/T]
ATCACCAAGGAGACCTAATGCTTCACATGCTGCCCGAAATGTAGGATATTCATGACCTGATATAGTTCTGATTTCAGCAAAGGATCTAGGGCCCTTAACG

Reverse complement sequence

CGTTAAGGGCCCTAGATCCTTTGCTGAAATCAGAACTATATCAGGTCATGAATATCCTACATTTCGGGCAGCATGTGAAGCATTAGGTCTCCTTGGTGAT[G/A]
ACCAAGAGTGGTCAAATGCTTTGAAAGATGCAGCTCAATGGGCCTTACCATCCCAACTGTGACAACTTTTTGTTACAATGTTACTCTTTTGTGAGGTAAC

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 99.70% 0.20% 0.13% 0.00% NA
All Indica  2759 99.40% 0.40% 0.22% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.40% 0.40% 0.22% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 0.80% 0.64% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0508103725 C -> T LOC_Os05g14380.1 upstream_gene_variant ; 28.0bp to feature; MODIFIER N Average:21.056; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N
vg0508103725 C -> T LOC_Os05g14390.1 upstream_gene_variant ; 875.0bp to feature; MODIFIER N Average:21.056; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N
vg0508103725 C -> T LOC_Os05g14380-LOC_Os05g14390 intergenic_region ; MODIFIER N Average:21.056; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0508103725 4.05E-06 NA mr1625 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