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Detailed information for vg0500831203:

Variant ID: vg0500831203 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 831203
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


CCCACACACCGGCAGCGCCAACACACACGACCAGGAGAAGGTTAGCACCAGACCGGCCGCCGCTAGACCAACAAAGGAACACAGACGAGATCGCCCTACA[G/A]
CAAGGGGGTGCCAAAACGACGTCTTCAAAAAGAGAAGCGACGGAAGACCGCCGCTGCCGTCCATCAGGGCTCAAAGGAGCCAAGACTGGGCTTTCGCCCG

Reverse complement sequence

CGGGCGAAAGCCCAGTCTTGGCTCCTTTGAGCCCTGATGGACGGCAGCGGCGGTCTTCCGTCGCTTCTCTTTTTGAAGACGTCGTTTTGGCACCCCCTTG[C/T]
TGTAGGGCGATCTCGTCTGTGTTCCTTTGTTGGTCTAGCGGCGGCCGGTCTGGTGCTAACCTTCTCCTGGTCGTGTGTGTTGGCGCTGCCGGTGTGTGGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.70% 9.30% 0.00% 0.00% NA
All Indica  2759 90.50% 9.50% 0.00% 0.00% NA
All Japonica  1512 91.90% 8.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 92.30% 7.70% 0.00% 0.00% NA
Indica III  913 85.40% 14.60% 0.00% 0.00% NA
Indica Intermediate  786 89.60% 10.40% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 78.80% 21.20% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 6.20% 0.00% 0.00% NA
VI/Aromatic  96 52.10% 47.90% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0500831203 G -> A LOC_Os05g02450.1 upstream_gene_variant ; 4391.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500831203 G -> A LOC_Os05g02450.2 upstream_gene_variant ; 4391.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500831203 G -> A LOC_Os05g02440.1 downstream_gene_variant ; 249.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500831203 G -> A LOC_Os05g02435-LOC_Os05g02440 intergenic_region ; 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
vg0500831203 3.36E-06 NA mr1754_2 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
vg0500831203 4.80E-06 2.73E-07 mr1754_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