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Detailed information for vg1015373114:

Variant ID: vg1015373114 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 15373114
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTAGACTGAGCACCGAGTTAAGCCTTACCCATTAGACATGTGGTTAGTACAATAGTGCTTTGCAACAGAGGCCCGAAGACCGATCCTTATAGTGGCCGA[A/G]
GTGCTACTAGCAGAACCATGCACCTCGAGCCCAGCCTAAAACCATTTTGGGAGTTTTGAATAGAGGGGGAGGGGGGGAGGTGTGTGTTCAATTCCATCAC

Reverse complement sequence

GTGATGGAATTGAACACACACCTCCCCCCCTCCCCCTCTATTCAAAACTCCCAAAATGGTTTTAGGCTGGGCTCGAGGTGCATGGTTCTGCTAGTAGCAC[T/C]
TCGGCCACTATAAGGATCGGTCTTCGGGCCTCTGTTGCAAAGCACTATTGTACTAACCACATGTCTAATGGGTAAGGCTTAACTCGGTGCTCAGTCTAGT

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 88.30% 11.20% 0.51% 0.00% NA
All Indica  2759 99.50% 0.40% 0.07% 0.00% NA
All Japonica  1512 65.10% 33.50% 1.46% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.70% 0.17% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.60% 0.13% 0.00% NA
Temperate Japonica  767 36.50% 61.00% 2.48% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 85.50% 13.30% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg1015373114 A -> G LOC_Os10g29580.1 upstream_gene_variant ; 1509.0bp to feature; MODIFIER silent_mutation Average:44.446; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg1015373114 A -> G LOC_Os10g29590.1 upstream_gene_variant ; 3305.0bp to feature; MODIFIER silent_mutation Average:44.446; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg1015373114 A -> G LOC_Os10g29560.1 downstream_gene_variant ; 4020.0bp to feature; MODIFIER silent_mutation Average:44.446; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg1015373114 A -> G LOC_Os10g29570.1 downstream_gene_variant ; 1923.0bp to feature; MODIFIER silent_mutation Average:44.446; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg1015373114 A -> G LOC_Os10g29570-LOC_Os10g29580 intergenic_region ; MODIFIER silent_mutation Average:44.446; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1015373114 NA 1.48E-12 Heading_date 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
vg1015373114 NA 9.19E-14 Spikelet_length 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
vg1015373114 3.52E-06 3.50E-06 mr1919_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
vg1015373114 NA 9.23E-06 mr1919_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