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Detailed information for vg0520857344:

Variant ID: vg0520857344 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 20857344
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGAGGAGAGAGGTGAGGAAGGTACGTGGTCTTTCTTTCCATCTCTCTGTTTATATGAGATTAAATCTAACGGTTAATATAATGGGCCCATCAATTTAAGT[G/A]
AAAGTGGATGGTTAGATGTTCTTTTCTCAGGATTTATAGTATTTTTTTAATTTATTAGAGTGCCACGTGACTGCTTAGGAGCGTTTGTAGATACTACATG

Reverse complement sequence

CATGTAGTATCTACAAACGCTCCTAAGCAGTCACGTGGCACTCTAATAAATTAAAAAAATACTATAAATCCTGAGAAAAGAACATCTAACCATCCACTTT[C/T]
ACTTAAATTGATGGGCCCATTATATTAACCGTTAGATTTAATCTCATATAAACAGAGAGATGGAAAGAAAGACCACGTACCTTCCTCACCTCTCTCCTCA

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 96.10% 3.40% 0.47% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 37.90% 53.90% 8.18% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 1.40% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0520857344 G -> A LOC_Os05g35110-LOC_Os05g35130 intergenic_region ; MODIFIER silent_mutation Average:40.202; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0520857344 1.87E-06 NA mr1248 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
vg0520857344 NA 2.00E-07 mr1706 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
vg0520857344 NA 1.81E-06 mr1815_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