| Variant ID: vg1209004627 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9004627 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAGCAGCGGCGCAATATGCCAGCCGTGAAGGCGAAGAGGCTTGTCGACGGAAGATGAGGCAGCTGGCAGTGTAGAATATGTCATTATCAGCCATGGCGAT[A/T]
AAGACAACATGTTTGGATAAATCCAATACACGGTATGGTAGGCGGAGCCTGCAGCTTGATTAATGTCATCGGCTGTCACCACAGCATTTGATAAACAAAG
CTTTGTTTATCAAATGCTGTGGTGACAGCCGATGACATTAATCAAGCTGCAGGCTCCGCCTACCATACCGTGTATTGGATTTATCCAAACATGTTGTCTT[T/A]
ATCGCCATGGCTGATAATGACATATTCTACACTGCCAGCTGCCTCATCTTCCGTCGACAAGCCTCTTCGCCTTCACGGCTGGCATATTGCGCCGCTGCTG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.50% | 0.20% | 0.51% | 20.82% | NA |
| All Indica | 2759 | 65.50% | 0.30% | 0.87% | 33.38% | NA |
| All Japonica | 1512 | 98.90% | 0.00% | 0.00% | 1.06% | NA |
| Aus | 269 | 87.00% | 0.00% | 0.00% | 13.01% | NA |
| Indica I | 595 | 58.50% | 0.00% | 1.68% | 39.83% | NA |
| Indica II | 465 | 65.40% | 0.90% | 1.08% | 32.69% | NA |
| Indica III | 913 | 68.20% | 0.00% | 0.00% | 31.76% | NA |
| Indica Intermediate | 786 | 67.60% | 0.50% | 1.15% | 30.79% | NA |
| Temperate Japonica | 767 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209004627 | A -> DEL | LOC_Os12g15770.1 | N | frameshift_variant | Average:44.861; most accessible tissue: Minghui63 flag leaf, score: 73.752 | N | N | N | N |
| vg1209004627 | A -> T | LOC_Os12g15770.1 | stop_gained ; p.Leu4*; HIGH | stop_gained | Average:44.861; most accessible tissue: Minghui63 flag leaf, score: 73.752 | N | N | N | N |