Variant ID: vg0220695059 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 20695059 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GAGCTAAGCCTTGACTTGAACTGCAGCGGGAACACCACTCCACAGGCATCCTCGACGGCACGGACAAAGCCTACTCCTCGGAGAAACCTTCATCTGACCC[A/G]
AACTCGAACTCTGGGGTTGGGAAAAGTAGAGCAAGACTGAGTACTACCCACTATACTCAGCAAGTCATACCGGAATAGGGGTATGATGCAGGGAATCATC
GATGATTCCCTGCATCATACCCCTATTCCGGTATGACTTGCTGAGTATAGTGGGTAGTACTCAGTCTTGCTCTACTTTTCCCAACCCCAGAGTTCGAGTT[T/C]
GGGTCAGATGAAGGTTTCTCCGAGGAGTAGGCTTTGTCCGTGCCGTCGAGGATGCCTGTGGAGTGGTGTTCCCGCTGCAGTTCAAGTCAAGGCTTAGCTC
Populations | Population Size | Frequency 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 |
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 |
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 |