| Variant ID: vg0415575690 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 15575690 |
| Reference Allele: TCCTCCTCCCCCTCCGCCACCTCCACTA | Alternative Allele: T |
| Primary Allele: TCCTCCTCCCCCTCCGCCAC CTCCACTA | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TAATATATAATCCTTCTTCCCTATCCTCTCCTCCACAACCGCCTCACACTTATCCTCTCAGATCGATCTCCCTCTTCTCCCTCTCAGATCGATCTCCCTC[TCCTCCTCCCCCTCCGCCACCTCCACTA/T]
CCTCCTCCCCCTCCGCCTCCTCCCCTTCCTCCTCCCATCCCCGGCCCTCTCCTCCCCGTCCTCCCTTCCCATCGCTCAGATCGATCTCCCTCTCCTCCTC
GAGGAGGAGAGGGAGATCGATCTGAGCGATGGGAAGGGAGGACGGGGAGGAGAGGGCCGGGGATGGGAGGAGGAAGGGGAGGAGGCGGAGGGGGAGGAGG[TAGTGGAGGTGGCGGAGGGGGAGGAGGA/A]
GAGGGAGATCGATCTGAGAGGGAGAAGAGGGAGATCGATCTGAGAGGATAAGTGTGAGGCGGTTGTGGAGGAGAGGATAGGGAAGAAGGATTATATATTA
| Populations | Population Size | Frequency of TCCTCCTCCCCCTCCGCCAC CTCCACTA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.40% | 9.80% | 3.03% | 20.69% | NA |
| All Indica | 2759 | 73.60% | 9.60% | 2.32% | 14.46% | NA |
| All Japonica | 1512 | 63.10% | 12.10% | 4.50% | 20.30% | NA |
| Aus | 269 | 3.70% | 0.40% | 2.60% | 93.31% | NA |
| Indica I | 595 | 83.20% | 7.70% | 0.67% | 8.40% | NA |
| Indica II | 465 | 62.60% | 8.20% | 3.01% | 26.24% | NA |
| Indica III | 913 | 72.90% | 11.40% | 2.96% | 12.71% | NA |
| Indica Intermediate | 786 | 73.70% | 9.80% | 2.42% | 14.12% | NA |
| Temperate Japonica | 767 | 51.40% | 6.00% | 4.56% | 38.07% | NA |
| Tropical Japonica | 504 | 74.60% | 20.60% | 3.77% | 0.99% | NA |
| Japonica Intermediate | 241 | 76.30% | 13.70% | 5.81% | 4.15% | NA |
| VI/Aromatic | 96 | 81.20% | 9.40% | 2.08% | 7.29% | NA |
| Intermediate | 90 | 74.40% | 7.80% | 2.22% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415575690 | TCCTCCTCCCCCTCCGCCACCTCCACTA -> DEL | N | N | silent_mutation | Average:39.066; most accessible tissue: Zhenshan97 flag leaf, score: 56.722 | N | N | N | N |
| vg0415575690 | TCCTCCTCCCCCTCCGCCACCTCCACTA -> T | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:39.066; most accessible tissue: Zhenshan97 flag leaf, score: 56.722 | N | N | N | N |