| Variant ID: vg0415575752 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 15575752 |
| Reference Allele: CCATCCCCGG | Alternative Allele: C |
| Primary Allele: CCATCCCCGG | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCGATCTCCCTCTTCTCCCTCTCAGATCGATCTCCCTCTCCTCCTCCCCCTCCGCCACCTCCACTACCTCCTCCCCCTCCGCCTCCTCCCCTTCCTCCTC[CCATCCCCGG/C]
CCCTCTCCTCCCCGTCCTCCCTTCCCATCGCTCAGATCGATCTCCCTCTCCTCCTCACCTCCTCCCTCTCAGATCGATCTCTCTCCTCCTCCCCCTCCAC
GTGGAGGGGGAGGAGGAGAGAGATCGATCTGAGAGGGAGGAGGTGAGGAGGAGAGGGAGATCGATCTGAGCGATGGGAAGGGAGGACGGGGAGGAGAGGG[CCGGGGATGG/G]
GAGGAGGAAGGGGAGGAGGCGGAGGGGGAGGAGGTAGTGGAGGTGGCGGAGGGGGAGGAGGAGAGGGAGATCGATCTGAGAGGGAGAAGAGGGAGATCGA
| Populations | Population Size | Frequency of CCATCCCCGG(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 79.80% | 0.00% | 2.58% | 17.60% | NA |
| All Indica | 2759 | 86.80% | 0.00% | 3.73% | 9.39% | NA |
| All Japonica | 1512 | 78.50% | 0.10% | 0.60% | 20.83% | NA |
| Aus | 269 | 8.60% | 0.00% | 2.97% | 88.48% | NA |
| Indica I | 595 | 92.40% | 0.00% | 5.55% | 2.02% | NA |
| Indica II | 465 | 75.70% | 0.00% | 1.72% | 22.58% | NA |
| Indica III | 913 | 88.70% | 0.00% | 3.94% | 7.34% | NA |
| Indica Intermediate | 786 | 87.00% | 0.10% | 3.31% | 9.54% | NA |
| Temperate Japonica | 767 | 60.10% | 0.00% | 1.04% | 38.85% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.40% | 0.41% | 4.56% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 1.04% | 6.25% | NA |
| Intermediate | 90 | 83.30% | 0.00% | 1.11% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415575752 | CCATCCCCGG -> C | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.305; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 | N | N | N | N |
| vg0415575752 | CCATCCCCGG -> DEL | N | N | silent_mutation | Average:44.305; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 | N | N | N | N |