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Detailed information for vg0220695059:

Variant ID: vg0220695059 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20695059
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGCTAAGCCTTGACTTGAACTGCAGCGGGAACACCACTCCACAGGCATCCTCGACGGCACGGACAAAGCCTACTCCTCGGAGAAACCTTCATCTGACCC[A/G]
AACTCGAACTCTGGGGTTGGGAAAAGTAGAGCAAGACTGAGTACTACCCACTATACTCAGCAAGTCATACCGGAATAGGGGTATGATGCAGGGAATCATC

Reverse complement sequence

GATGATTCCCTGCATCATACCCCTATTCCGGTATGACTTGCTGAGTATAGTGGGTAGTACTCAGTCTTGCTCTACTTTTCCCAACCCCAGAGTTCGAGTT[T/C]
GGGTCAGATGAAGGTTTCTCCGAGGAGTAGGCTTTGTCCGTGCCGTCGAGGATGCCTGTGGAGTGGTGTTCCCGCTGCAGTTCAAGTCAAGGCTTAGCTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 41.80% 8.60% 6.96% 42.59% NA
All Indica  2759 23.20% 1.40% 10.29% 65.06% NA
All Japonica  1512 75.50% 22.70% 0.53% 1.32% NA
Aus  269 18.60% 4.50% 11.90% 65.06% NA
Indica I  595 20.20% 0.00% 12.77% 67.06% NA
Indica II  465 18.10% 2.20% 9.03% 70.75% NA
Indica III  913 28.60% 1.30% 9.31% 60.79% NA
Indica Intermediate  786 22.40% 2.20% 10.31% 65.14% NA
Temperate Japonica  767 74.60% 23.70% 0.91% 0.78% NA
Tropical Japonica  504 78.20% 20.40% 0.00% 1.39% NA
Japonica Intermediate  241 72.60% 24.10% 0.41% 2.90% NA
VI/Aromatic  96 92.70% 3.10% 1.04% 3.12% NA
Intermediate  90 62.20% 11.10% 4.44% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0220695059 A -> G LOC_Os02g34520.1 downstream_gene_variant ; 922.0bp to feature; MODIFIER silent_mutation Average:18.271; most accessible tissue: Minghui63 young leaf, score: 39.381 N N N N
vg0220695059 A -> G LOC_Os02g34520-LOC_Os02g34530 intergenic_region ; MODIFIER silent_mutation Average:18.271; most accessible tissue: Minghui63 young leaf, score: 39.381 N N N N
vg0220695059 A -> DEL N N silent_mutation Average:18.271; most accessible tissue: Minghui63 young leaf, score: 39.381 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220695059 1.20E-06 NA Grain_weight 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