| Variant ID: vg0410565219 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 10565219 |
| Reference Allele: TACTCCCGGTC | Alternative Allele: T |
| Primary Allele: TACTCCCGGTC | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AACAAATCTCTGCCAACCAACAACTTTCCAAATAGCACGAAAATCAACATCCATACCTATCTTTTTCAGCAGCTCCGGAGAGTATTCTCGTGTGTGAGCA[TACTCCCGGTC/T]
ACTCAGCATGTAGTAGGCTTGTCTTTCCCGATCGTCGACAAGGTCGAGGTCGGCGTCATTCAAGAGACGTCGTGGAGCTTCGGCATCCTCCATCGAGACT
AGTCTCGATGGAGGATGCCGAAGCTCCACGACGTCTCTTGAATGACGCCGACCTCGACCTTGTCGACGATCGGGAAAGACAAGCCTACTACATGCTGAGT[GACCGGGAGTA/A]
TGCTCACACACGAGAATACTCTCCGGAGCTGCTGAAAAAGATAGGTATGGATGTTGATTTTCGTGCTATTTGGAAAGTTGTTGGTTGGCAGAGATTTGTT
| Populations | Population Size | Frequency of TACTCCCGGTC(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 28.60% | 12.00% | 0.61% | 58.87% | NA |
| All Indica | 2759 | 8.80% | 0.50% | 0.83% | 89.85% | NA |
| All Japonica | 1512 | 64.50% | 34.90% | 0.00% | 0.66% | NA |
| Aus | 269 | 5.20% | 0.00% | 1.12% | 93.68% | NA |
| Indica I | 595 | 5.70% | 0.20% | 0.84% | 93.28% | NA |
| Indica II | 465 | 24.90% | 1.30% | 0.65% | 73.12% | NA |
| Indica III | 913 | 2.30% | 0.30% | 0.55% | 96.82% | NA |
| Indica Intermediate | 786 | 9.00% | 0.60% | 1.27% | 89.06% | NA |
| Temperate Japonica | 767 | 96.50% | 3.40% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 12.10% | 86.90% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 72.20% | 26.10% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 82.30% | 6.20% | 0.00% | 11.46% | NA |
| Intermediate | 90 | 44.40% | 18.90% | 3.33% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410565219 | TACTCCCGGTC -> DEL | LOC_Os04g19010.1 | N | frameshift_variant | Average:9.854; most accessible tissue: Callus, score: 40.877 | N | N | N | N |
| vg0410565219 | TACTCCCGGTC -> T | LOC_Os04g19010.1 | frameshift_variant ; p.Asp32fs; HIGH | frameshift_variant | Average:9.854; most accessible tissue: Callus, score: 40.877 | N | N | N | N |