| Variant ID: vg1218481506 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481506 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CGTTGCCATGTTTTGATCTCCAACGAAGCTTTGCCGTCGACTCCGTGGTCGCCGGACCTCGCCGTATCCACTGTCGGCATCGCAGCAGTGAGGAGAAGCC[T/C]
GGCAGCCACCTCCGCGAAGACGCAAGCCATCGGAGCACCGTCGTCCCCGTGAAGCCGATCTGTTCCATCTTCAGTCGCGCCGTTCGTTGTCGTCCGTCGT
ACGACGGACGACAACGAACGGCGCGACTGAAGATGGAACAGATCGGCTTCACGGGGACGACGGTGCTCCGATGGCTTGCGTCTTCGCGGAGGTGGCTGCC[A/G]
GGCTTCTCCTCACTGCTGCGATGCCGACAGTGGATACGGCGAGGTCCGGCGACCACGGAGTCGACGGCAAAGCTTCGTTGGAGATCAAAACATGGCAACG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 12.70% | 0.10% | 2.88% | 84.28% | NA |
| All Indica | 2759 | 2.00% | 0.00% | 1.49% | 96.56% | NA |
| All Japonica | 1512 | 34.30% | 0.30% | 0.40% | 65.01% | NA |
| Aus | 269 | 1.50% | 0.00% | 31.97% | 66.54% | NA |
| Indica I | 595 | 2.90% | 0.00% | 0.84% | 96.30% | NA |
| Indica II | 465 | 3.20% | 0.00% | 1.94% | 94.84% | NA |
| Indica III | 913 | 0.20% | 0.00% | 0.77% | 99.01% | NA |
| Indica Intermediate | 786 | 2.50% | 0.00% | 2.54% | 94.91% | NA |
| Temperate Japonica | 767 | 59.50% | 0.00% | 0.26% | 40.29% | NA |
| Tropical Japonica | 504 | 2.80% | 0.00% | 0.20% | 97.02% | NA |
| Japonica Intermediate | 241 | 19.90% | 2.10% | 1.24% | 76.76% | NA |
| VI/Aromatic | 96 | 0.00% | 1.00% | 1.04% | 97.92% | NA |
| Intermediate | 90 | 27.80% | 0.00% | 2.22% | 70.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481506 | T -> C | LOC_Os12g30780.1 | missense_variant ; p.Arg11Gly; MODERATE | nonsynonymous_codon ; R11G | Average:20.187; most accessible tissue: Callus, score: 29.312 | unknown | unknown | TOLERATED | 1.00 |
| vg1218481506 | T -> DEL | LOC_Os12g30780.1 | N | frameshift_variant | Average:20.187; most accessible tissue: Callus, score: 29.312 | N | N | N | N |