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Detailed information for vg0525619564:

Variant ID: vg0525619564 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 25619564
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGCAACCAGTTTGAAATATGGAAATACTCCTACGGGAGTGTTTAGTTTACACCAAAATTAAAAGTTTGGTTGAAATTAGAACGATGTGATGGAAAAGTT[G/A]
AAAGTTTATGTGTGTATGAAAGTTTTGATGTGATAGAAAAGTCGGAAGTTTGAAAAAATATTTTGAAACTAAACACGGCCTATGTATATGAAGTCCACGT

Reverse complement sequence

ACGTGGACTTCATATACATAGGCCGTGTTTAGTTTCAAAATATTTTTTCAAACTTCCGACTTTTCTATCACATCAAAACTTTCATACACACATAAACTTT[C/T]
AACTTTTCCATCACATCGTTCTAATTTCAACCAAACTTTTAATTTTGGTGTAAACTAAACACTCCCGTAGGAGTATTTCCATATTTCAAACTGGTTGCTA

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 94.30% 3.60% 2.12% 0.00% NA
All Indica  2759 99.70% 0.20% 0.07% 0.00% NA
All Japonica  1512 84.60% 9.30% 6.15% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.30% 0.13% 0.00% NA
Temperate Japonica  767 88.50% 2.90% 8.60% 0.00% NA
Tropical Japonica  504 94.00% 4.80% 1.19% 0.00% NA
Japonica Intermediate  241 52.30% 39.00% 8.71% 0.00% NA
VI/Aromatic  96 75.00% 21.90% 3.12% 0.00% NA
Intermediate  90 94.40% 3.30% 2.22% 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
vg0525619564 G -> A LOC_Os05g44050.1 upstream_gene_variant ; 987.0bp to feature; MODIFIER silent_mutation Average:46.182; most accessible tissue: Callus, score: 79.734 N N N N
vg0525619564 G -> A LOC_Os05g44060.1 upstream_gene_variant ; 4459.0bp to feature; MODIFIER silent_mutation Average:46.182; most accessible tissue: Callus, score: 79.734 N N N N
vg0525619564 G -> A LOC_Os05g44030.1 downstream_gene_variant ; 1263.0bp to feature; MODIFIER silent_mutation Average:46.182; most accessible tissue: Callus, score: 79.734 N N N N
vg0525619564 G -> A LOC_Os05g44030-LOC_Os05g44050 intergenic_region ; MODIFIER silent_mutation Average:46.182; most accessible tissue: Callus, score: 79.734 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0525619564 2.18E-06 NA Plant_height Jap_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
vg0525619564 NA 6.43E-06 mr1180 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
vg0525619564 NA 3.24E-07 mr1180_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
vg0525619564 NA 4.46E-07 mr1183_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