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Detailed information for vg0410565071:

Variant ID: vg0410565071 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 10565071
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATCGTGAAAACCAAGAAGTGTACTTAATCCTTTCCATGTAAGTGTGTATTCCTTATGGAAAAATCAAAAGGAAATTCCATCTTCTATTTCTTTCAAAGT[G/A]
CACAGAAATTGCAAAGTAAGCAAAAGAGAACCAGGCTCATCTACCACAACAAATCTCTGCCAACCAACAACTTTCCAAATAGCACGAAAATCAACATCCA

Reverse complement sequence

TGGATGTTGATTTTCGTGCTATTTGGAAAGTTGTTGGTTGGCAGAGATTTGTTGTGGTAGATGAGCCTGGTTCTCTTTTGCTTACTTTGCAATTTCTGTG[C/T]
ACTTTGAAAGAAATAGAAGATGGAATTTCCTTTTGATTTTTCCATAAGGAATACACACTTACATGGAAAGGATTAAGTACACTTCTTGGTTTTCACGATT

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 24.40% 15.00% 0.32% 60.26% NA
All Indica  2759 7.40% 0.70% 0.47% 91.41% NA
All Japonica  1512 61.00% 38.20% 0.07% 0.79% NA
Aus  269 0.40% 0.00% 0.37% 99.26% NA
Indica I  595 5.00% 0.20% 1.01% 93.78% NA
Indica II  465 24.10% 1.30% 0.43% 74.19% NA
Indica III  913 1.50% 0.40% 0.11% 97.92% NA
Indica Intermediate  786 6.10% 1.10% 0.51% 92.24% NA
Temperate Japonica  767 96.00% 3.70% 0.00% 0.39% NA
Tropical Japonica  504 4.20% 94.60% 0.20% 0.99% NA
Japonica Intermediate  241 68.50% 29.90% 0.00% 1.66% NA
VI/Aromatic  96 0.00% 86.50% 0.00% 13.54% NA
Intermediate  90 30.00% 32.20% 0.00% 37.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0410565071 G -> DEL LOC_Os04g19010.1 N frameshift_variant Average:9.325; most accessible tissue: Callus, score: 40.117 N N N N
vg0410565071 G -> A LOC_Os04g19010.1 synonymous_variant ; p.Cys84Cys; LOW synonymous_codon Average:9.325; most accessible tissue: Callus, score: 40.117 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0410565071 NA 3.82E-06 mr1045 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
vg0410565071 NA 2.17E-06 mr1090 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
vg0410565071 NA 3.42E-06 mr1121 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
vg0410565071 NA 9.29E-08 mr1194 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
vg0410565071 NA 1.11E-06 mr1206 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
vg0410565071 NA 4.91E-07 mr1206 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
vg0410565071 NA 1.64E-13 mr1330 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
vg0410565071 NA 5.73E-07 mr1403 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
vg0410565071 NA 3.88E-08 mr1449 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
vg0410565071 NA 4.87E-14 mr1454 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
vg0410565071 NA 3.88E-11 mr1454 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
vg0410565071 NA 2.90E-07 mr1642 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
vg0410565071 NA 3.67E-07 mr1715 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
vg0410565071 NA 3.57E-07 mr1739 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
vg0410565071 NA 3.46E-13 mr1789 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
vg0410565071 NA 6.15E-06 mr1844 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
vg0410565071 NA 4.95E-12 mr1864 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
vg0410565071 NA 2.12E-09 mr1880 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
vg0410565071 NA 1.21E-09 mr1398_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
vg0410565071 NA 8.97E-14 mr1454_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