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Detailed information for vg0522137809:

Variant ID: vg0522137809 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 22137809
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCCTCTACAGCTCGCCCGCTGCCGCCGTTCTTTATTATCATTGAGATTTTAAAATAAAAAATGATTATCATTGGGGTTTTTTTTTTTTACTTTTTAGAA[G/A,T]
CCCGAACCTTTAAAAAGTGAAACTTCTTATAGTTTTTAGAGTTTTATTGTCTCGATGGATTTCATGTTTTTTATAATTTTTAGAAATCCCGTCAAACACT

Reverse complement sequence

AGTGTTTGACGGGATTTCTAAAAATTATAAAAAACATGAAATCCATCGAGACAATAAAACTCTAAAAACTATAAGAAGTTTCACTTTTTAAAGGTTCGGG[C/T,A]
TTCTAAAAAGTAAAAAAAAAAAACCCCAATGATAATCATTTTTTATTTTAAAATCTCAATGATAATAAAGAACGGCGGCAGCGGGCGAGCTGTAGAGGAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.90% 0.40% 0.25% 0.00% A: 0.36%
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 97.80% 1.40% 0.73% 0.00% A: 0.13%
Aus  269 94.80% 0.00% 0.00% 0.00% A: 5.20%
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 96.70% 2.00% 1.30% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 96.70% 2.50% 0.00% 0.00% A: 0.83%
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 0.00% 0.00% A: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0522137809 G -> T LOC_Os05g37800.1 upstream_gene_variant ; 2237.0bp to feature; MODIFIER silent_mutation Average:31.614; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0522137809 G -> T LOC_Os05g37790-LOC_Os05g37800 intergenic_region ; MODIFIER silent_mutation Average:31.614; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0522137809 G -> A LOC_Os05g37800.1 upstream_gene_variant ; 2237.0bp to feature; MODIFIER silent_mutation Average:31.614; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0522137809 G -> A LOC_Os05g37790-LOC_Os05g37800 intergenic_region ; MODIFIER silent_mutation Average:31.614; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0522137809 NA 2.37E-08 Awn_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0522137809 4.16E-07 6.04E-07 mr1274 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
vg0522137809 NA 1.81E-06 mr1274_2 Jap_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
vg0522137809 NA 2.15E-06 mr1549_2 Jap_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
vg0522137809 NA 7.93E-07 mr1757_2 Jap_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