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Detailed information for vg0605613230:

Variant ID: vg0605613230 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5613230
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGTTTCACAACGTAAATCATTCTAGCATTTTTCATATTCATATTGATGCTAATGAATCTAAATTCATTAGCATCATTATGAATGTGGGAAATGCTAGAAT[A/G]
ATCTAGATTCATTAGTATCAATATGAATATGGGAAATGCTAGAATGATTTACATTGTGAAACGGAGAAAGTATATTTATAATTGACGAAAACATTGTATA

Reverse complement sequence

TATACAATGTTTTCGTCAATTATAAATATACTTTCTCCGTTTCACAATGTAAATCATTCTAGCATTTCCCATATTCATATTGATACTAATGAATCTAGAT[T/C]
ATTCTAGCATTTCCCACATTCATAATGATGCTAATGAATTTAGATTCATTAGCATCAATATGAATATGAAAAATGCTAGAATGATTTACGTTGTGAAACG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.40% 4.70% 0.97% 0.00% NA
All Indica  2759 99.60% 0.40% 0.04% 0.00% NA
All Japonica  1512 89.60% 7.50% 2.91% 0.00% NA
Aus  269 96.30% 3.30% 0.37% 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 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.60% 0.13% 0.00% NA
Temperate Japonica  767 83.20% 11.50% 5.35% 0.00% NA
Tropical Japonica  504 99.40% 0.40% 0.20% 0.00% NA
Japonica Intermediate  241 89.60% 9.50% 0.83% 0.00% NA
VI/Aromatic  96 15.60% 84.40% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0605613230 A -> G LOC_Os06g10750.1 upstream_gene_variant ; 769.0bp to feature; MODIFIER silent_mutation Average:63.72; most accessible tissue: Callus, score: 85.848 N N N N
vg0605613230 A -> G LOC_Os06g10740.1 downstream_gene_variant ; 1793.0bp to feature; MODIFIER silent_mutation Average:63.72; most accessible tissue: Callus, score: 85.848 N N N N
vg0605613230 A -> G LOC_Os06g10740-LOC_Os06g10750 intergenic_region ; MODIFIER silent_mutation Average:63.72; most accessible tissue: Callus, score: 85.848 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0605613230 5.36E-09 NA mr1210 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
vg0605613230 7.90E-07 3.26E-09 mr1210 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
vg0605613230 1.13E-06 NA mr1305 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
vg0605613230 NA 3.99E-07 mr1305 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
vg0605613230 1.31E-06 1.51E-12 mr1585 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
vg0605613230 9.34E-06 8.22E-10 mr1585 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
vg0605613230 8.73E-09 NA mr1586 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
vg0605613230 1.43E-06 9.13E-09 mr1586 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
vg0605613230 NA 7.59E-07 mr1127_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
vg0605613230 6.63E-10 NA mr1305_2 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
vg0605613230 1.32E-07 4.60E-10 mr1305_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
vg0605613230 3.14E-06 NA mr1409_2 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
vg0605613230 5.18E-07 2.73E-08 mr1409_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
vg0605613230 NA 4.16E-06 mr1559_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
vg0605613230 6.48E-07 3.57E-14 mr1585_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
vg0605613230 4.90E-06 5.53E-10 mr1585_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
vg0605613230 2.92E-06 NA mr1765_2 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
vg0605613230 NA 8.69E-07 mr1765_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
vg0605613230 7.17E-06 NA mr1980_2 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