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Detailed information for vg0518262212:

Variant ID: vg0518262212 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 18262212
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.01, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


GTTTGACACAAGGTTGGGGTGCGACGATCGAGGGTCTTCCTCATCGCGCTCCACAACCAACGCTGCGCTAATCACTTGCAGAGTTGCCGCTAAGTAAAGT[A/T]
GCAGCGGTTCCTCTGGCTCCGGGGCTACCAAGATTGGAGGAGAGTTGAGGTAAGCCTTTAATTGATTCAATGCCTGCTCGGCCTCCTTTGTCCAGACAAA

Reverse complement sequence

TTTGTCTGGACAAAGGAGGCCGAGCAGGCATTGAATCAATTAAAGGCTTACCTCAACTCTCCTCCAATCTTGGTAGCCCCGGAGCCAGAGGAACCGCTGC[T/A]
ACTTTACTTAGCGGCAACTCTGCAAGTGATTAGCGCAGCGTTGGTTGTGGAGCGCGATGAGGAAGACCCTCGATCGTCGCACCCCAACCTTGTGTCAAAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.30% 12.80% 2.94% 0.00% NA
All Indica  2759 74.20% 20.90% 4.86% 0.00% NA
All Japonica  1512 98.70% 1.10% 0.13% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 79.00% 8.60% 12.44% 0.00% NA
Indica II  465 72.00% 24.10% 3.87% 0.00% NA
Indica III  913 79.20% 20.20% 0.66% 0.00% NA
Indica Intermediate  786 66.20% 29.30% 4.58% 0.00% NA
Temperate Japonica  767 98.00% 1.70% 0.26% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 10.00% 3.33% 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
vg0518262212 A -> T LOC_Os05g31400.1 downstream_gene_variant ; 358.0bp to feature; MODIFIER silent_mutation Average:74.448; most accessible tissue: Zhenshan97 young leaf, score: 86.383 N N N N
vg0518262212 A -> T LOC_Os05g31410.1 downstream_gene_variant ; 1895.0bp to feature; MODIFIER silent_mutation Average:74.448; most accessible tissue: Zhenshan97 young leaf, score: 86.383 N N N N
vg0518262212 A -> T LOC_Os05g31400-LOC_Os05g31410 intergenic_region ; MODIFIER silent_mutation Average:74.448; most accessible tissue: Zhenshan97 young leaf, score: 86.383 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0518262212 NA 2.15E-07 mr1238_2 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
vg0518262212 NA 9.93E-07 mr1407_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
vg0518262212 NA 1.23E-07 mr1484_2 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
vg0518262212 NA 8.59E-06 mr1609_2 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
vg0518262212 NA 5.22E-07 mr1900_2 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
vg0518262212 2.14E-06 2.14E-06 mr1945_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