| Variant ID: vg0415575704 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15575704 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCTTCCCTATCCTCTCCTCCACAACCGCCTCACACTTATCCTCTCAGATCGATCTCCCTCTTCTCCCTCTCAGATCGATCTCCCTCTCCTCCTCCCCCTC[C/T]
GCCACCTCCACTACCTCCTCCCCCTCCGCCTCCTCCCCTTCCTCCTCCCATCCCCGGCCCTCTCCTCCCCGTCCTCCCTTCCCATCGCTCAGATCGATCT
AGATCGATCTGAGCGATGGGAAGGGAGGACGGGGAGGAGAGGGCCGGGGATGGGAGGAGGAAGGGGAGGAGGCGGAGGGGGAGGAGGTAGTGGAGGTGGC[G/A]
GAGGGGGAGGAGGAGAGGGAGATCGATCTGAGAGGGAGAAGAGGGAGATCGATCTGAGAGGATAAGTGTGAGGCGGTTGTGGAGGAGAGGATAGGGAAGA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.90% | 6.60% | 0.47% | 22.01% | NA |
| All Indica | 2759 | 72.30% | 11.20% | 0.43% | 16.02% | NA |
| All Japonica | 1512 | 78.40% | 0.00% | 0.53% | 21.10% | NA |
| Aus | 269 | 4.80% | 0.00% | 0.00% | 95.17% | NA |
| Indica I | 595 | 90.10% | 0.30% | 0.34% | 9.24% | NA |
| Indica II | 465 | 68.80% | 4.10% | 0.22% | 26.88% | NA |
| Indica III | 913 | 59.50% | 24.60% | 0.55% | 15.33% | NA |
| Indica Intermediate | 786 | 75.80% | 8.10% | 0.51% | 15.52% | NA |
| Temperate Japonica | 767 | 60.00% | 0.00% | 0.65% | 39.37% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.20% | 0.99% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.00% | 0.83% | 4.98% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 76.70% | 4.40% | 2.22% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415575704 | C -> DEL | N | N | silent_mutation | Average:40.322; most accessible tissue: Zhenshan97 young leaf, score: 59.009 | N | N | N | N |
| vg0415575704 | C -> T | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:40.322; most accessible tissue: Zhenshan97 young leaf, score: 59.009 | N | N | N | N |