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Detailed information for vg1003725590:

Variant ID: vg1003725590 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3725590
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.19, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


TGGGGCCCGCCTGCCAGCCGCACTCCATCCCGCCTTGTGCCACTGCCAGTGGGGGCCCACGTGCCGGCGTCCCTCCCTCTCTCTCTCGAGCCACTGACCC[G/A]
TGGGGCCCACCTGTTGGCGCCGCCCCCTTTTTGCTGACGTCAGCCCTGGGATGAGTTATTGCGCAATAAATTGATTAAGGGTTTTTCTTTTATAGTAAAA

Reverse complement sequence

TTTTACTATAAAAGAAAAACCCTTAATCAATTTATTGCGCAATAACTCATCCCAGGGCTGACGTCAGCAAAAAGGGGGCGGCGCCAACAGGTGGGCCCCA[C/T]
GGGTCAGTGGCTCGAGAGAGAGAGGGAGGGACGCCGGCACGTGGGCCCCCACTGGCAGTGGCACAAGGCGGGATGGAGTGCGGCTGGCAGGCGGGCCCCA

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 42.70% 38.30% 0.13% 18.87% NA
All Indica  2759 23.90% 44.90% 0.18% 30.99% NA
All Japonica  1512 76.90% 22.90% 0.00% 0.13% NA
Aus  269 30.50% 68.40% 0.00% 1.12% NA
Indica I  595 18.00% 65.70% 0.17% 16.13% NA
Indica II  465 41.50% 33.10% 0.00% 25.38% NA
Indica III  913 19.80% 29.60% 0.11% 50.49% NA
Indica Intermediate  786 22.60% 54.10% 0.38% 22.90% NA
Temperate Japonica  767 98.80% 1.00% 0.00% 0.13% NA
Tropical Japonica  504 39.90% 60.10% 0.00% 0.00% NA
Japonica Intermediate  241 84.60% 14.90% 0.00% 0.41% NA
VI/Aromatic  96 71.90% 1.00% 1.04% 26.04% NA
Intermediate  90 51.10% 41.10% 0.00% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1003725590 G -> A LOC_Os10g07080.1 upstream_gene_variant ; 2375.0bp to feature; MODIFIER silent_mutation Average:32.011; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg1003725590 G -> A LOC_Os10g07060-LOC_Os10g07080 intergenic_region ; MODIFIER silent_mutation Average:32.011; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg1003725590 G -> DEL N N silent_mutation Average:32.011; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003725590 NA 1.13E-07 Grain_thickness Ind_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
vg1003725590 NA 5.32E-06 mr1073 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
vg1003725590 NA 1.04E-08 mr1217 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
vg1003725590 NA 3.92E-06 mr1304 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
vg1003725590 NA 3.02E-06 mr1388 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
vg1003725590 NA 9.25E-06 mr1407 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
vg1003725590 NA 8.11E-08 mr1414 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
vg1003725590 NA 8.75E-07 mr1606 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
vg1003725590 NA 6.77E-07 mr1646 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
vg1003725590 NA 2.33E-06 mr1830 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
vg1003725590 NA 5.85E-08 mr1845 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
vg1003725590 NA 7.27E-06 mr1200_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