| Variant ID: vg0415575794 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15575794 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCTCCCCCTCCGCCACCTCCACTACCTCCTCCCCCTCCGCCTCCTCCCCTTCCTCCTCCCATCCCCGGCCCTCTCCTCCCCGTCCTCCCTTCCCATCGCT[C/T]
AGATCGATCTCCCTCTCCTCCTCACCTCCTCCCTCTCAGATCGATCTCTCTCCTCCTCCCCCTCCACCTCCTCCCCTTCCCATCCCATCCCCGGCCCTAT
ATAGGGCCGGGGATGGGATGGGAAGGGGAGGAGGTGGAGGGGGAGGAGGAGAGAGATCGATCTGAGAGGGAGGAGGTGAGGAGGAGAGGGAGATCGATCT[G/A]
AGCGATGGGAAGGGAGGACGGGGAGGAGAGGGCCGGGGATGGGAGGAGGAAGGGGAGGAGGCGGAGGGGGAGGAGGTAGTGGAGGTGGCGGAGGGGGAGG
| 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 | 77.40% | 0.10% | 1.63% | 20.84% | NA |
| All Indica | 2759 | 83.30% | 0.30% | 2.21% | 14.21% | NA |
| All Japonica | 1512 | 78.20% | 0.00% | 0.40% | 21.36% | NA |
| Aus | 269 | 5.20% | 0.00% | 2.23% | 92.57% | NA |
| Indica I | 595 | 90.30% | 0.30% | 0.84% | 8.57% | NA |
| Indica II | 465 | 70.10% | 0.00% | 4.09% | 25.81% | NA |
| Indica III | 913 | 85.00% | 0.30% | 2.30% | 12.38% | NA |
| Indica Intermediate | 786 | 84.00% | 0.30% | 2.04% | 13.74% | NA |
| Temperate Japonica | 767 | 59.60% | 0.00% | 0.52% | 39.90% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 0.83% | 4.56% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 80.00% | 0.00% | 4.44% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415575794 | C -> DEL | N | N | silent_mutation | Average:44.678; most accessible tissue: Zhenshan97 young leaf, score: 66.83 | N | N | N | N |
| vg0415575794 | C -> T | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.678; most accessible tissue: Zhenshan97 young leaf, score: 66.83 | N | N | N | N |