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Detailed information for vg0525173806:

Variant ID: vg0525173806 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 25173806
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


AAGGGGTTCAACCACCACTAACCACATCAACCAAACAAGGCAGGGCCACATTGAGGAAGAGAAGTGCAGCACCCAAGAAGAAAAACTCTCCCAAGAAAAA[G/A]
AAACAGTAGTTTATACTATGCATTCATAAAGTTGGTTCCATGTTATCGATTTTGAGCGACCTTACTAGTGCACAATCAAATTCATGTCAAGTTATGCATT

Reverse complement sequence

AATGCATAACTTGACATGAATTTGATTGTGCACTAGTAAGGTCGCTCAAAATCGATAACATGGAACCAACTTTATGAATGCATAGTATAAACTACTGTTT[C/T]
TTTTTCTTGGGAGAGTTTTTCTTCTTGGGTGCTGCACTTCTCTTCCTCAATGTGGCCCTGCCTTGTTTGGTTGATGTGGTTAGTGGTGGTTGAACCCCTT

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 87.40% 12.00% 0.63% 0.00% NA
All Indica  2759 97.10% 2.80% 0.11% 0.00% NA
All Japonica  1512 88.60% 9.80% 1.65% 0.00% NA
Aus  269 6.30% 93.70% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.10% 0.60% 0.22% 0.00% NA
Indica III  913 97.80% 2.20% 0.00% 0.00% NA
Indica Intermediate  786 93.10% 6.60% 0.25% 0.00% NA
Temperate Japonica  767 95.30% 3.30% 1.43% 0.00% NA
Tropical Japonica  504 88.70% 10.90% 0.40% 0.00% NA
Japonica Intermediate  241 66.80% 28.20% 4.98% 0.00% NA
VI/Aromatic  96 17.70% 81.20% 1.04% 0.00% NA
Intermediate  90 84.40% 14.40% 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
vg0525173806 G -> A LOC_Os05g43280.1 upstream_gene_variant ; 2845.0bp to feature; MODIFIER silent_mutation Average:29.461; most accessible tissue: Minghui63 flower, score: 39.692 N N N N
vg0525173806 G -> A LOC_Os05g43252.1 downstream_gene_variant ; 4512.0bp to feature; MODIFIER silent_mutation Average:29.461; most accessible tissue: Minghui63 flower, score: 39.692 N N N N
vg0525173806 G -> A LOC_Os05g43252.2 downstream_gene_variant ; 4513.0bp to feature; MODIFIER silent_mutation Average:29.461; most accessible tissue: Minghui63 flower, score: 39.692 N N N N
vg0525173806 G -> A LOC_Os05g43252-LOC_Os05g43280 intergenic_region ; MODIFIER silent_mutation Average:29.461; most accessible tissue: Minghui63 flower, score: 39.692 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0525173806 NA 2.91E-10 mr1465 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
vg0525173806 2.04E-06 NA mr1563_2 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
vg0525173806 NA 1.59E-06 mr1929_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