| Variant ID: vg0415575876 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15575876 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCCTCCCTTCCCATCGCTCAGATCGATCTCCCTCTCCTCCTCACCTCCTCCCTCTCAGATCGATCTCTCTCCTCCTCCCCCTCCACCTCCTCCCCTTCCC[A/C]
TCCCATCCCCGGCCCTATCCTCCCCCTCCTCCCTTCCCACGTGGGAGGTGGCCGGCTGGGCCGCGCACGGGCCCAGTGGCGAGCGGCGGCAGGCAGCAGC
GCTGCTGCCTGCCGCCGCTCGCCACTGGGCCCGTGCGCGGCCCAGCCGGCCACCTCCCACGTGGGAAGGGAGGAGGGGGAGGATAGGGCCGGGGATGGGA[T/G]
GGGAAGGGGAGGAGGTGGAGGGGGAGGAGGAGAGAGATCGATCTGAGAGGGAGGAGGTGAGGAGGAGAGGGAGATCGATCTGAGCGATGGGAAGGGAGGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.40% | 6.70% | 0.66% | 22.24% | NA |
| All Indica | 2759 | 71.90% | 11.30% | 0.54% | 16.27% | NA |
| All Japonica | 1512 | 78.20% | 0.00% | 0.46% | 21.36% | NA |
| Aus | 269 | 3.70% | 0.00% | 1.12% | 95.17% | NA |
| Indica I | 595 | 89.60% | 0.30% | 0.67% | 9.41% | NA |
| Indica II | 465 | 68.20% | 4.30% | 0.22% | 27.31% | NA |
| Indica III | 913 | 58.70% | 24.80% | 0.99% | 15.55% | NA |
| Indica Intermediate | 786 | 76.10% | 8.00% | 0.13% | 15.78% | NA |
| Temperate Japonica | 767 | 59.60% | 0.00% | 0.65% | 39.77% | 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 | 87.50% | 1.00% | 3.12% | 8.33% | NA |
| Intermediate | 90 | 75.60% | 4.40% | 3.33% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415575876 | A -> C | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:41.653; most accessible tissue: Zhenshan97 young leaf, score: 61.964 | N | N | N | N |
| vg0415575876 | A -> DEL | N | N | silent_mutation | Average:41.653; most accessible tissue: Zhenshan97 young leaf, score: 61.964 | N | N | N | N |