| Variant ID: vg0435226336 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 35226336 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GAGGGTCGAAGGATCCACGACTTCGACATCCACGGGTGATGGGGAAGGGCGGCGAGATGGGGAGCGTCGCCTCCTCGTCTACGGCGACGGTAGCACGCCC[C/T]
AGGGCGCGCTCCAAGCTGCGGGCGCGCTCCTACGTCACCCGCCCATTGTCCCTGACCCGGAGTCTCCAGCCCAACGTTGGCTGGACGACGTGGCCAACTT
AAGTTGGCCACGTCGTCCAGCCAACGTTGGGCTGGAGACTCCGGGTCAGGGACAATGGGCGGGTGACGTAGGAGCGCGCCCGCAGCTTGGAGCGCGCCCT[G/A]
GGGCGTGCTACCGTCGCCGTAGACGAGGAGGCGACGCTCCCCATCTCGCCGCCCTTCCCCATCACCCGTGGATGTCGAAGTCGTGGATCCTTCGACCCTC
| 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 | 46.00% | 0.10% | 1.99% | 51.86% | NA |
| All Indica | 2759 | 11.20% | 0.00% | 2.17% | 86.66% | NA |
| All Japonica | 1512 | 96.80% | 0.40% | 2.05% | 0.79% | NA |
| Aus | 269 | 91.10% | 0.00% | 0.00% | 8.92% | NA |
| Indica I | 595 | 7.20% | 0.00% | 1.85% | 90.92% | NA |
| Indica II | 465 | 5.60% | 0.00% | 1.08% | 93.33% | NA |
| Indica III | 913 | 10.10% | 0.00% | 3.07% | 86.86% | NA |
| Indica Intermediate | 786 | 18.70% | 0.00% | 2.04% | 79.26% | NA |
| Temperate Japonica | 767 | 97.80% | 0.80% | 1.30% | 0.13% | NA |
| Tropical Japonica | 504 | 96.20% | 0.00% | 1.98% | 1.79% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 4.56% | 0.83% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 1.04% | 9.38% | NA |
| Intermediate | 90 | 81.10% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0435226336 | C -> DEL | LOC_Os04g59220.1 | N | frameshift_variant | Average:7.909; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0435226336 | C -> T | LOC_Os04g59220.1 | stop_gained ; p.Gln79*; HIGH | stop_gained | Average:7.909; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |