| Variant ID: vg0221510773 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 21510773 |
| Reference Allele: TG | Alternative Allele: T |
| Primary Allele: TG | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GAGAGGCCCCCGAGCCGAACGGCGGCCTAAGGCCCCCGACGACCGGAGCTGGCCCTCCGCCTGCTTGTCCGACGGTGCCAGGCGCCCCCGACCCCCAGGA[TG/T]
GCCCCGAGGCCACTGCGGGAAGGCCGCGCCTGTCGCCCTCTGACCCCGAGGTCGTCGGCACAGAAGCCGAATGCGCCCCGCGTGGCCTCTCGGATGGAGA
TCTCCATCCGAGAGGCCACGCGGGGCGCATTCGGCTTCTGTGCCGACGACCTCGGGGTCAGAGGGCGACAGGCGCGGCCTTCCCGCAGTGGCCTCGGGGC[CA/A]
TCCTGGGGGTCGGGGGCGCCTGGCACCGTCGGACAAGCAGGCGGAGGGCCAGCTCCGGTCGTCGGGGGCCTTAGGCCGCCGTTCGGCTCGGGGGCCTCTC
| Populations | Population Size | Frequency of TG(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.80% | 0.10% | 1.18% | 63.94% | NA |
| All Indica | 2759 | 2.20% | 0.00% | 1.01% | 96.74% | NA |
| All Japonica | 1512 | 95.30% | 0.30% | 1.46% | 2.91% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.00% | 99.63% | NA |
| Indica I | 595 | 2.00% | 0.00% | 0.84% | 97.14% | NA |
| Indica II | 465 | 2.60% | 0.00% | 1.08% | 96.34% | NA |
| Indica III | 913 | 1.80% | 0.00% | 0.55% | 97.70% | NA |
| Indica Intermediate | 786 | 2.80% | 0.00% | 1.65% | 95.55% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 1.17% | 1.04% | NA |
| Tropical Japonica | 504 | 92.70% | 0.40% | 0.79% | 6.15% | NA |
| Japonica Intermediate | 241 | 92.90% | 1.20% | 3.73% | 2.07% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 3.12% | 6.25% | NA |
| Intermediate | 90 | 57.80% | 0.00% | 3.33% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221510773 | TG -> T | LOC_Os02g35800.1 | frameshift_variant ; p.Gly596fs; HIGH | frameshift_variant | Average:13.691; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0221510773 | TG -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:13.691; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |