| Variant ID: vg0415575861 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15575861 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCCCTCTCCTCCCCGTCCTCCCTTCCCATCGCTCAGATCGATCTCCCTCTCCTCCTCACCTCCTCCCTCTCAGATCGATCTCTCTCCTCCTCCCCCTCCA[C/T]
CTCCTCCCCTTCCCATCCCATCCCCGGCCCTATCCTCCCCCTCCTCCCTTCCCACGTGGGAGGTGGCCGGCTGGGCCGCGCACGGGCCCAGTGGCGAGCG
CGCTCGCCACTGGGCCCGTGCGCGGCCCAGCCGGCCACCTCCCACGTGGGAAGGGAGGAGGGGGAGGATAGGGCCGGGGATGGGATGGGAAGGGGAGGAG[G/A]
TGGAGGGGGAGGAGGAGAGAGATCGATCTGAGAGGGAGGAGGTGAGGAGGAGAGGGAGATCGATCTGAGCGATGGGAAGGGAGGACGGGGAGGAGAGGGC
| 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 | 70.80% | 6.60% | 0.47% | 22.09% | NA |
| All Indica | 2759 | 72.20% | 11.20% | 0.51% | 16.09% | NA |
| All Japonica | 1512 | 78.30% | 0.00% | 0.40% | 21.30% | NA |
| Aus | 269 | 5.20% | 0.00% | 0.00% | 94.80% | NA |
| Indica I | 595 | 89.60% | 0.30% | 0.67% | 9.41% | NA |
| Indica II | 465 | 68.60% | 4.30% | 0.22% | 26.88% | NA |
| Indica III | 913 | 59.50% | 24.40% | 0.77% | 15.33% | NA |
| Indica Intermediate | 786 | 76.10% | 8.00% | 0.25% | 15.65% | NA |
| Temperate Japonica | 767 | 59.80% | 0.00% | 0.52% | 39.63% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.20% | 0.99% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.00% | 0.41% | 5.39% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0415575861 | C -> DEL | N | N | silent_mutation | Average:41.652; most accessible tissue: Zhenshan97 young leaf, score: 62.534 | N | N | N | N |
| vg0415575861 | C -> T | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:41.652; most accessible tissue: Zhenshan97 young leaf, score: 62.534 | N | N | N | N |