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Detailed information for vg0500736167:

Variant ID: vg0500736167 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 736167
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.78, A: 0.22, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:


AAATTTGCTAGTTTATTTTTAGTTTCGCCGTACTATTAAGAGGGGTAATGACCTAGCAAAGAGATGATTTTAATTGCCACATTAGGTCATTGTGCATTTA[G/A]
ACTTGTGCTCGTTTTTCATCACACACACAATCACTTGGGATTTCACTGGTTTCGGCGTGACCAGGGGCAGTCAGACTGGCCACATAGTGGCGGTCTGACC

Reverse complement sequence

GGTCAGACCGCCACTATGTGGCCAGTCTGACTGCCCCTGGTCACGCCGAAACCAGTGAAATCCCAAGTGATTGTGTGTGTGATGAAAAACGAGCACAAGT[C/T]
TAAATGCACAATGACCTAATGTGGCAATTAAAATCATCTCTTTGCTAGGTCATTACCCCTCTTAATAGTACGGCGAAACTAAAAATAAACTAGCAAATTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 44.50% 33.10% 13.08% 9.31% NA
All Indica  2759 66.30% 3.60% 21.28% 8.81% NA
All Japonica  1512 4.20% 87.60% 0.20% 8.00% NA
Aus  269 58.70% 30.10% 6.32% 4.83% NA
Indica I  595 97.30% 0.70% 0.84% 1.18% NA
Indica II  465 69.90% 7.70% 11.61% 10.75% NA
Indica III  913 39.00% 3.30% 44.80% 12.92% NA
Indica Intermediate  786 72.40% 3.80% 15.14% 8.65% NA
Temperate Japonica  767 6.80% 92.70% 0.00% 0.52% NA
Tropical Japonica  504 0.00% 79.00% 0.60% 20.44% NA
Japonica Intermediate  241 5.00% 89.20% 0.00% 5.81% NA
VI/Aromatic  96 25.00% 10.40% 8.33% 56.25% NA
Intermediate  90 31.10% 55.60% 3.33% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0500736167 G -> DEL N N silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500736167 G -> A LOC_Os05g02300.1 upstream_gene_variant ; 2037.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500736167 G -> A LOC_Os05g02280.1 downstream_gene_variant ; 3987.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500736167 G -> A LOC_Os05g02290.1 downstream_gene_variant ; 889.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500736167 G -> A LOC_Os05g02310.1 downstream_gene_variant ; 3479.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500736167 G -> A LOC_Os05g02290-LOC_Os05g02300 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
vg0500736167 NA 9.31E-06 mr1750 Ind_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
vg0500736167 NA 4.34E-06 mr1991 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
vg0500736167 NA 8.32E-07 mr1321_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
vg0500736167 1.15E-07 NA mr1750_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