| Variant ID: vg1218481256 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481256 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAAGGACCCCCTAGTCGTCCTCTACCCATCCCCTCAAGTCCCGTCCGCCGCCATCGCCGGAAACGCTCTCCCCGCGAGCTCCCTCTCTCTCCACCTCCGG[C/T]
AGCCGCTCCAGCTGCCGTGCGCCGTCGCCCCGGCCGTCGCCGGTCAGCGCCGCCACTTCCCTCGGCTCCGCAAAGTCGAGCTCTACCCCGGCCACCCGTT
AACGGGTGGCCGGGGTAGAGCTCGACTTTGCGGAGCCGAGGGAAGTGGCGGCGCTGACCGGCGACGGCCGGGGCGACGGCGCACGGCAGCTGGAGCGGCT[G/A]
CCGGAGGTGGAGAGAGAGGGAGCTCGCGGGGAGAGCGTTTCCGGCGATGGCGGCGGACGGGACTTGAGGGGATGGGTAGAGGACGACTAGGGGGTCCTTT
| 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 | 34.30% | 0.10% | 9.65% | 55.90% | NA |
| All Indica | 2759 | 29.50% | 0.00% | 13.08% | 57.38% | NA |
| All Japonica | 1512 | 39.40% | 0.00% | 1.46% | 59.13% | NA |
| Aus | 269 | 57.60% | 1.50% | 13.38% | 27.51% | NA |
| Indica I | 595 | 16.00% | 0.00% | 11.09% | 72.94% | NA |
| Indica II | 465 | 31.60% | 0.00% | 10.75% | 57.63% | NA |
| Indica III | 913 | 36.80% | 0.00% | 15.22% | 47.97% | NA |
| Indica Intermediate | 786 | 30.20% | 0.00% | 13.49% | 56.36% | NA |
| Temperate Japonica | 767 | 61.00% | 0.00% | 0.65% | 38.33% | NA |
| Tropical Japonica | 504 | 10.90% | 0.00% | 1.39% | 87.70% | NA |
| Japonica Intermediate | 241 | 30.30% | 0.00% | 4.15% | 65.56% | NA |
| VI/Aromatic | 96 | 15.60% | 2.10% | 25.00% | 57.29% | NA |
| Intermediate | 90 | 44.40% | 1.10% | 14.44% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481256 | C -> DEL | N | N | silent_mutation | Average:36.879; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
| vg1218481256 | C -> T | LOC_Os12g30770.1 | upstream_gene_variant ; 1943.0bp to feature; MODIFIER | silent_mutation | Average:36.879; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
| vg1218481256 | C -> T | LOC_Os12g30790.1 | downstream_gene_variant ; 3650.0bp to feature; MODIFIER | silent_mutation | Average:36.879; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
| vg1218481256 | C -> T | LOC_Os12g30780.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.879; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |