| Variant ID: vg0811599249 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 11599249 |
| Reference Allele: GC | Alternative Allele: G |
| Primary Allele: GC | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGGGAGCCGCTTGAGGGTCCCGGCCATCTCTGAGAGGCGCTGGGCGAG[GC/G]
CCCCCTGGTTGGCGGCGTACTTCGCGTACCGCCCGCCCCAGAGGCCCGCCTGCCGCCCGGCACGGTCTAGACGGGAGACGGCATCCCGAAGCATGCCGGG
CCCGGCATGCTTCGGGATGCCGTCTCCCGTCTAGACCGTGCCGGGCGGCAGGCGGGCCTCTGGGGCGGGCGGTACGCGAAGTACGCCGCCAACCAGGGGG[GC/C]
CTCGCCCAGCGCCTCTCAGAGATGGCCGGGACCCTCAAGCGGCTCCCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGG
| 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 | 47.90% | 0.40% | 2.81% | 48.92% | NA |
| All Indica | 2759 | 54.00% | 0.00% | 2.03% | 43.97% | NA |
| All Japonica | 1512 | 36.50% | 0.90% | 4.50% | 58.13% | NA |
| Aus | 269 | 51.30% | 1.10% | 1.49% | 46.10% | NA |
| Indica I | 595 | 32.60% | 0.00% | 4.20% | 63.19% | NA |
| Indica II | 465 | 37.40% | 0.00% | 1.94% | 60.65% | NA |
| Indica III | 913 | 78.40% | 0.00% | 0.99% | 20.59% | NA |
| Indica Intermediate | 786 | 51.50% | 0.10% | 1.65% | 46.69% | NA |
| Temperate Japonica | 767 | 27.40% | 0.10% | 6.13% | 66.36% | NA |
| Tropical Japonica | 504 | 48.40% | 1.80% | 2.98% | 46.83% | NA |
| Japonica Intermediate | 241 | 40.70% | 1.20% | 2.49% | 55.60% | NA |
| VI/Aromatic | 96 | 47.90% | 1.00% | 2.08% | 48.96% | NA |
| Intermediate | 90 | 42.20% | 0.00% | 3.33% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599249 | GC -> G | LOC_Os08g19400.1 | frameshift_variant ; p.Gly218fs; HIGH | frameshift_variant | Average:20.279; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |
| vg0811599249 | GC -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:20.279; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |