| Variant ID: vg0415575789 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 15575789 |
| Reference Allele: T | Alternative Allele: TC |
| Primary Allele: T | Secondary Allele: TC |
Inferred Ancestral Allele: Not determined.
CTCCTCCTCCCCCTCCGCCACCTCCACTACCTCCTCCCCCTCCGCCTCCTCCCCTTCCTCCTCCCATCCCCGGCCCTCTCCTCCCCGTCCTCCCTTCCCA[T/TC]
CGCTCAGATCGATCTCCCTCTCCTCCTCACCTCCTCCCTCTCAGATCGATCTCTCTCCTCCTCCCCCTCCACCTCCTCCCCTTCCCATCCCATCCCCGGC
GCCGGGGATGGGATGGGAAGGGGAGGAGGTGGAGGGGGAGGAGGAGAGAGATCGATCTGAGAGGGAGGAGGTGAGGAGGAGAGGGAGATCGATCTGAGCG[A/GA]
TGGGAAGGGAGGACGGGGAGGAGAGGGCCGGGGATGGGAGGAGGAAGGGGAGGAGGCGGAGGGGGAGGAGGTAGTGGAGGTGGCGGAGGGGGAGGAGGAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.50% | 0.20% | 1.31% | 20.95% | NA |
| All Indica | 2759 | 83.50% | 0.30% | 2.14% | 14.03% | NA |
| All Japonica | 1512 | 78.40% | 0.00% | 0.07% | 21.49% | NA |
| Aus | 269 | 4.80% | 0.00% | 0.74% | 94.42% | NA |
| Indica I | 595 | 91.60% | 0.30% | 1.85% | 6.22% | NA |
| Indica II | 465 | 70.10% | 0.00% | 3.66% | 26.24% | NA |
| Indica III | 913 | 84.40% | 0.30% | 2.19% | 13.03% | NA |
| Indica Intermediate | 786 | 84.20% | 0.50% | 1.40% | 13.87% | NA |
| Temperate Japonica | 767 | 59.80% | 0.00% | 0.00% | 40.16% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.20% | 0.99% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.00% | 0.00% | 4.98% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 81.10% | 0.00% | 0.00% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415575789 | T -> DEL | N | N | silent_mutation | Average:44.678; most accessible tissue: Zhenshan97 young leaf, score: 66.83 | N | N | N | N |
| vg0415575789 | T -> TC | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.678; most accessible tissue: Zhenshan97 young leaf, score: 66.83 | N | N | N | N |