| Variant ID: vg0415575757 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15575757 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTCCCTCTTCTCCCTCTCAGATCGATCTCCCTCTCCTCCTCCCCCTCCGCCACCTCCACTACCTCCTCCCCCTCCGCCTCCTCCCCTTCCTCCTCCCATC[C/A]
CCGGCCCTCTCCTCCCCGTCCTCCCTTCCCATCGCTCAGATCGATCTCCCTCTCCTCCTCACCTCCTCCCTCTCAGATCGATCTCTCTCCTCCTCCCCCT
AGGGGGAGGAGGAGAGAGATCGATCTGAGAGGGAGGAGGTGAGGAGGAGAGGGAGATCGATCTGAGCGATGGGAAGGGAGGACGGGGAGGAGAGGGCCGG[G/T]
GATGGGAGGAGGAAGGGGAGGAGGCGGAGGGGGAGGAGGTAGTGGAGGTGGCGGAGGGGGAGGAGGAGAGGGAGATCGATCTGAGAGGGAGAAGAGGGAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 79.50% | 0.10% | 2.41% | 17.99% | NA |
| All Indica | 2759 | 86.30% | 0.20% | 3.41% | 10.08% | NA |
| All Japonica | 1512 | 78.60% | 0.00% | 0.66% | 20.77% | NA |
| Aus | 269 | 8.60% | 0.00% | 2.97% | 88.48% | NA |
| Indica I | 595 | 91.80% | 0.00% | 4.71% | 3.53% | NA |
| Indica II | 465 | 75.50% | 0.00% | 2.37% | 22.15% | NA |
| Indica III | 913 | 88.00% | 0.30% | 3.61% | 8.11% | NA |
| Indica Intermediate | 786 | 86.80% | 0.30% | 2.80% | 10.18% | NA |
| Temperate Japonica | 767 | 60.00% | 0.00% | 1.30% | 38.72% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0415575757 | C -> DEL | N | N | silent_mutation | Average:44.068; most accessible tissue: Zhenshan97 young leaf, score: 63.653 | N | N | N | N |
| vg0415575757 | C -> A | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.068; most accessible tissue: Zhenshan97 young leaf, score: 63.653 | N | N | N | N |