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Detailed information for vg0427390584:

Variant ID: vg0427390584 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 27390584
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAAAGTAAACTGGTCACTGAAAGTCTGCTGCAGTAGTCTTTTACTAAAAGAGAACAATTACCTGCAGTCCTATATATTAGTATATTATTTCGCACAAAAT[A/G]
ATAATTAAATCTTGACCTAATCTCATAACCAGCATTTAGCCGGATGATTTGCGCAGAAACCCATCAAAGCTAGCTAGCCACTGCAGAGAGACGCAACAAG

Reverse complement sequence

CTTGTTGCGTCTCTCTGCAGTGGCTAGCTAGCTTTGATGGGTTTCTGCGCAAATCATCCGGCTAAATGCTGGTTATGAGATTAGGTCAAGATTTAATTAT[T/C]
ATTTTGTGCGAAATAATATACTAATATATAGGACTGCAGGTAATTGTTCTCTTTTAGTAAAAGACTACTGCAGCAGACTTTCAGTGACCAGTTTACTTTA

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 67.70% 32.20% 0.08% 0.00% NA
All Indica  2759 92.70% 7.20% 0.07% 0.00% NA
All Japonica  1512 19.80% 80.00% 0.13% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 90.80% 9.10% 0.17% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 93.00% 7.00% 0.00% 0.00% NA
Indica Intermediate  786 91.00% 8.90% 0.13% 0.00% NA
Temperate Japonica  767 7.40% 92.40% 0.13% 0.00% NA
Tropical Japonica  504 24.20% 75.60% 0.20% 0.00% NA
Japonica Intermediate  241 50.20% 49.80% 0.00% 0.00% NA
VI/Aromatic  96 27.10% 72.90% 0.00% 0.00% NA
Intermediate  90 53.30% 46.70% 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
vg0427390584 A -> G LOC_Os04g46220-LOC_Os04g46240 intergenic_region ; MODIFIER silent_mutation Average:53.193; most accessible tissue: Callus, score: 77.538 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0427390584 NA 1.04E-17 mr1767 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
vg0427390584 NA 3.62E-08 mr1137_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
vg0427390584 NA 3.61E-07 mr1212_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
vg0427390584 NA 2.88E-06 mr1227_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
vg0427390584 7.15E-06 7.15E-06 mr1574_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
vg0427390584 5.96E-06 2.27E-07 mr1617_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
vg0427390584 NA 1.43E-06 mr1745_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