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Detailed information for vg0527031350:

Variant ID: vg0527031350 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 27031350
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: 286. )

Flanking Sequence (100 bp) in Reference Genome:


GCATCAAGGCTCCCCTGATTAGCTAATTACTCAGCCAGGGGTGTCCCATTCCACCCATGTGGTTGCACTATCATATGCTTGGATATAATTCCGAAGGAAT[C/T]
GGTCCTTAAATGCGACCGCACAAGCATCCCGCCTAGGAATGGCCTTGTGTCACGAGTTTTATTTTTAAAGCTCATTTTCTTTCACAAGGCACCGACCCAG

Reverse complement sequence

CTGGGTCGGTGCCTTGTGAAAGAAAATGAGCTTTAAAAATAAAACTCGTGACACAAGGCCATTCCTAGGCGGGATGCTTGTGCGGTCGCATTTAAGGACC[G/A]
ATTCCTTCGGAATTATATCCAAGCATATGATAGTGCAACCACATGGGTGGAATGGGACACCCCTGGCTGAGTAATTAGCTAATCAGGGGAGCCTTGATGC

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 97.60% 1.70% 0.70% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 92.60% 5.20% 2.18% 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 86.40% 9.50% 4.04% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 2.50% 0.83% 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
vg0527031350 C -> T LOC_Os05g46690.1 upstream_gene_variant ; 4235.0bp to feature; MODIFIER silent_mutation Average:37.793; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 N N N N
vg0527031350 C -> T LOC_Os05g46700.1 upstream_gene_variant ; 1581.0bp to feature; MODIFIER silent_mutation Average:37.793; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 N N N N
vg0527031350 C -> T LOC_Os05g46690-LOC_Os05g46700 intergenic_region ; MODIFIER silent_mutation Average:37.793; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0527031350 3.72E-06 3.72E-06 mr1477 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