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Detailed information for vg0203321613:

Variant ID: vg0203321613 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 3321613
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAAGCTTAATTGCTTCATGATTTGACAATGTGGTGCTACAGTAAACATTTGCTAATGATGGATTAATTAGGCTTGATAAATTCGTCTCGTAGTTTACAT[G/A]
CGGATTCTGTAATTTGTTTGGTTATTAAACTATATTTAATACTTTAAATGTGTATATGTATATTTGATGTGACACAGTAAAAAACTTTACCCATAAATCT

Reverse complement sequence

AGATTTATGGGTAAAGTTTTTTACTGTGTCACATCAAATATACATATACACATTTAAAGTATTAAATATAGTTTAATAACCAAACAAATTACAGAATCCG[C/T]
ATGTAAACTACGAGACGAATTTATCAAGCCTAATTAATCCATCATTAGCAAATGTTTACTGTAGCACCACATTGTCAAATCATGAAGCAATTAAGCTTAA

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 96.80% 2.80% 0.47% 0.00% NA
All Indica  2759 99.80% 0.00% 0.18% 0.00% NA
All Japonica  1512 90.90% 8.10% 0.99% 0.00% NA
Aus  269 98.90% 0.70% 0.37% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.00% 0.25% 0.00% NA
Temperate Japonica  767 98.60% 0.90% 0.52% 0.00% NA
Tropical Japonica  504 78.20% 20.20% 1.59% 0.00% NA
Japonica Intermediate  241 92.90% 5.80% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 1.11% 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
vg0203321613 G -> A LOC_Os02g06600.1 upstream_gene_variant ; 1625.0bp to feature; MODIFIER silent_mutation Average:44.36; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N
vg0203321613 G -> A LOC_Os02g06592.1 downstream_gene_variant ; 3228.0bp to feature; MODIFIER silent_mutation Average:44.36; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N
vg0203321613 G -> A LOC_Os02g06592-LOC_Os02g06600 intergenic_region ; MODIFIER silent_mutation Average:44.36; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0203321613 NA 1.35E-06 Grain_weight 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
vg0203321613 NA 1.36E-08 mr1040 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
vg0203321613 NA 2.73E-06 mr1156 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
vg0203321613 NA 3.52E-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
vg0203321613 NA 5.01E-06 mr1437 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
vg0203321613 NA 9.77E-06 mr1636 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
vg0203321613 NA 4.09E-06 mr1836_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