| Variant ID: vg1218481304 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481304 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGCCATCGCCGGAAACGCTCTCCCCGCGAGCTCCCTCTCTCTCCACCTCCGGCAGCCGCTCCAGCTGCCGTGCGCCGTCGCCCCGGCCGTCGCCGGTCAG[C/T]
GCCGCCACTTCCCTCGGCTCCGCAAAGTCGAGCTCTACCCCGGCCACCCGTTCTTTTGCGCTGAACCCCGCCGGAAGTCGCCGTCACCGTGAAGGCCGAA
TTCGGCCTTCACGGTGACGGCGACTTCCGGCGGGGTTCAGCGCAAAAGAACGGGTGGCCGGGGTAGAGCTCGACTTTGCGGAGCCGAGGGAAGTGGCGGC[G/A]
CTGACCGGCGACGGCCGGGGCGACGGCGCACGGCAGCTGGAGCGGCTGCCGGAGGTGGAGAGAGAGGGAGCTCGCGGGGAGAGCGTTTCCGGCGATGGCG
| 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 | 14.80% | 2.40% | 7.36% | 75.39% | NA |
| All Indica | 2759 | 4.70% | 3.60% | 8.34% | 83.40% | NA |
| All Japonica | 1512 | 35.50% | 0.30% | 1.85% | 62.30% | NA |
| Aus | 269 | 1.90% | 3.70% | 27.51% | 66.91% | NA |
| Indica I | 595 | 4.00% | 1.30% | 4.87% | 89.75% | NA |
| Indica II | 465 | 7.30% | 3.70% | 7.53% | 81.51% | NA |
| Indica III | 913 | 3.20% | 5.40% | 10.84% | 80.61% | NA |
| Indica Intermediate | 786 | 5.50% | 3.10% | 8.52% | 82.95% | NA |
| Temperate Japonica | 767 | 59.60% | 0.00% | 0.91% | 39.50% | NA |
| Tropical Japonica | 504 | 4.20% | 0.80% | 2.98% | 92.06% | NA |
| Japonica Intermediate | 241 | 24.50% | 0.40% | 2.49% | 72.61% | NA |
| VI/Aromatic | 96 | 2.10% | 1.00% | 7.29% | 89.58% | NA |
| Intermediate | 90 | 28.90% | 1.10% | 10.00% | 60.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481304 | C -> DEL | N | N | silent_mutation | Average:35.824; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg1218481304 | C -> T | LOC_Os12g30770.1 | upstream_gene_variant ; 1991.0bp to feature; MODIFIER | silent_mutation | Average:35.824; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg1218481304 | C -> T | LOC_Os12g30790.1 | downstream_gene_variant ; 3602.0bp to feature; MODIFIER | silent_mutation | Average:35.824; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg1218481304 | C -> T | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:35.824; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |