| Variant ID: vg0137499722 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 37499722 |
| Reference Allele: GC | Alternative Allele: G |
| Primary Allele: GC | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCTCCCCCATCTTACGGGGCCACTTCTTCTTGCGCTCCCCCTCGGGCTGCGATGTTGGCGCGGCCCCCTCCGGGCGCCTGTTACTGGCACGCGCCGCCCC[GC/G]
CCCCTCGGGGAGGAGATGGGGGAAGTGTTCCTCCCTGCTTCCTCTTCCCCCGGGCGTTGGCAGGGCGGCTGCTCCCCGGGCCCCTGTCGCGGGACCCAGA
TCTGGGTCCCGCGACAGGGGCCCGGGGAGCAGCCGCCCTGCCAACGCCCGGGGGAAGAGGAAGCAGGGAGGAACACTTCCCCCATCTCCTCCCCGAGGGG[GC/C]
GGGGCGGCGCGTGCCAGTAACAGGCGCCCGGAGGGGGCCGCGCCAACATCGCAGCCCGAGGGGGAGCGCAAGAAGAAGTGGCCCCGTAAGATGGGGGAGA
| Populations | Population Size | Frequency of GC(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.70% | 0.20% | 0.19% | 63.90% | NA |
| All Indica | 2759 | 2.30% | 0.00% | 0.14% | 97.54% | NA |
| All Japonica | 1512 | 97.30% | 0.50% | 0.13% | 2.05% | NA |
| Aus | 269 | 0.70% | 0.00% | 0.74% | 98.51% | NA |
| Indica I | 595 | 1.20% | 0.00% | 0.17% | 98.66% | NA |
| Indica II | 465 | 1.30% | 0.00% | 0.00% | 98.71% | NA |
| Indica III | 913 | 1.10% | 0.00% | 0.11% | 98.80% | NA |
| Indica Intermediate | 786 | 5.20% | 0.00% | 0.25% | 94.53% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.00% | 1.69% | NA |
| Tropical Japonica | 504 | 97.40% | 0.00% | 0.00% | 2.58% | NA |
| Japonica Intermediate | 241 | 93.80% | 3.30% | 0.83% | 2.07% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 64.40% | 0.00% | 1.11% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137499722 | GC -> G | LOC_Os01g64610.1 | frameshift_variant ; p.Gly332fs; HIGH | frameshift_variant | Average:6.37; most accessible tissue: Callus, score: 17.235 | N | N | N | N |
| vg0137499722 | GC -> DEL | LOC_Os01g64610.1 | N | frameshift_variant | Average:6.37; most accessible tissue: Callus, score: 17.235 | N | N | N | N |