| Variant ID: vg1120445314 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20445314 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCAGTTGTTAAGATATAAATAGGCATGCTCAAGGGCAGAGAGGTTCTCCAGGCCAAAATCCACATGATCATGTGTCTTGTGCACATCGATGAATAATTTA[A/T]
GTGTTCGAAGATTCTGCATGGCTCCTTGTGCAAACTCGATCTCCATGGTGTCACTCCAGTACTCGAAAAGTGATAGGCACTTGAATCGGTAGCTGATTAT
ATAATCAGCTACCGATTCAAGTGCCTATCACTTTTCGAGTACTGGAGTGACACCATGGAGATCGAGTTTGCACAAGGAGCCATGCAGAATCTTCGAACAC[T/A]
TAAATTATTCATCGATGTGCACAAGACACATGATCATGTGGATTTTGGCCTGGAGAACCTCTCTGCCCTTGAGCATGCCTATTTATATCTTAACAACTGC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.40% | 0.20% | 1.61% | 19.72% | NA |
| All Indica | 2759 | 70.70% | 0.40% | 2.07% | 26.82% | NA |
| All Japonica | 1512 | 95.40% | 0.00% | 0.99% | 3.64% | NA |
| Aus | 269 | 55.00% | 0.00% | 1.49% | 43.49% | NA |
| Indica I | 595 | 53.40% | 0.00% | 3.03% | 43.53% | NA |
| Indica II | 465 | 80.20% | 0.00% | 2.80% | 16.99% | NA |
| Indica III | 913 | 70.50% | 1.20% | 1.64% | 26.62% | NA |
| Indica Intermediate | 786 | 78.40% | 0.00% | 1.40% | 20.23% | NA |
| Temperate Japonica | 767 | 97.00% | 0.00% | 1.69% | 1.30% | NA |
| Tropical Japonica | 504 | 91.10% | 0.00% | 0.40% | 8.53% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 0.00% | 12.50% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120445314 | A -> T | LOC_Os11g34880.1 | missense_variant ; p.Leu525His; MODERATE | nonsynonymous_codon ; L525H | Average:43.046; most accessible tissue: Callus, score: 91.905 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1120445314 | A -> DEL | LOC_Os11g34880.1 | N | frameshift_variant | Average:43.046; most accessible tissue: Callus, score: 91.905 | N | N | N | N |