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Detailed information for vg0503613659:

Variant ID: vg0503613659 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 3613659
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGCAAAAAAAAAAGTTTCTATACGAAAGTTGCTTAAAAAAATCATATTGATCTATTTTTGAAAAAAAATAGCCAATACTTAATTAATCACGTGCTAATA[A/G]
ACCGCTCCGTTTTTCGTGCGCACTGATCTGGTTGGGAACGCTGGCTTCCGAACACAGCTATGTTCGCCATTACCAGTTCCCAACCGGAATAGTACGCACA

Reverse complement sequence

TGTGCGTACTATTCCGGTTGGGAACTGGTAATGGCGAACATAGCTGTGTTCGGAAGCCAGCGTTCCCAACCAGATCAGTGCGCACGAAAAACGGAGCGGT[T/C]
TATTAGCACGTGATTAATTAAGTATTGGCTATTTTTTTTCAAAAATAGATCAATATGATTTTTTTAAGCAACTTTCGTATAGAAACTTTTTTTTTTGCAA

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 89.20% 10.60% 0.15% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 68.20% 31.40% 0.40% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 46.70% 52.90% 0.39% 0.00% NA
Tropical Japonica  504 93.50% 6.20% 0.40% 0.00% NA
Japonica Intermediate  241 83.80% 15.80% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 83.30% 15.60% 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
vg0503613659 A -> G LOC_Os05g06900.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:64.093; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0503613659 A -> G LOC_Os05g06910.1 upstream_gene_variant ; 978.0bp to feature; MODIFIER silent_mutation Average:64.093; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0503613659 A -> G LOC_Os05g06890.1 downstream_gene_variant ; 2288.0bp to feature; MODIFIER silent_mutation Average:64.093; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0503613659 NA 6.19E-13 Grain_thickness 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
vg0503613659 7.69E-08 2.22E-16 Heading_date All YES 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
vg0503613659 NA 3.32E-13 Heading_date 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
vg0503613659 NA 2.11E-12 Plant_height 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
vg0503613659 NA 6.83E-18 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
vg0503613659 NA 2.14E-12 Spikelet_length 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
vg0503613659 NA 1.14E-06 mr1354 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
vg0503613659 NA 2.40E-06 mr1359_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
vg0503613659 NA 1.75E-09 mr1486_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
vg0503613659 NA 3.63E-08 mr1588_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