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Detailed information for vg0500304693:

Variant ID: vg0500304693 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 304693
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.77, C: 0.23, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


GACTAACTTTTTTTCTCGAACGTACAGGAGAGCTGCGTGTCATTCCATTAAACAAACAGTACATCACAACCTACATTCCATTAAAACAGACACGCCACAG[A/C]
AGAAAAAAGTGACCAAAGGACACTAGAGATCTAAACTATCCCGAGTTCCTGACCCATAAACTCTCAAGATCTTTAGCTCCAGTTGCCATCTACATCAGAA

Reverse complement sequence

TTCTGATGTAGATGGCAACTGGAGCTAAAGATCTTGAGAGTTTATGGGTCAGGAACTCGGGATAGTTTAGATCTCTAGTGTCCTTTGGTCACTTTTTTCT[T/G]
CTGTGGCGTGTCTGTTTTAATGGAATGTAGGTTGTGATGTACTGTTTGTTTAATGGAATGACACGCAGCTCTCCTGTACGTTCGAGAAAAAAAGTTAGTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 77.50% 22.40% 0.04% 0.00% NA
All Indica  2759 70.40% 29.60% 0.04% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 45.00% 55.00% 0.00% 0.00% NA
Indica I  595 94.10% 5.90% 0.00% 0.00% NA
Indica II  465 66.00% 34.00% 0.00% 0.00% NA
Indica III  913 61.60% 38.40% 0.00% 0.00% NA
Indica Intermediate  786 65.30% 34.60% 0.13% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 30.20% 69.80% 0.00% 0.00% NA
Intermediate  90 80.00% 18.90% 1.11% 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
vg0500304693 A -> C LOC_Os05g01510.1 downstream_gene_variant ; 929.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500304693 A -> C LOC_Os05g01510.2 downstream_gene_variant ; 929.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500304693 A -> C LOC_Os05g01520.1 intron_variant ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0500304693 NA 8.72E-11 mr1531_2 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