| Variant ID: vg0602220624 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 2220624 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGAACGAGGCGCAGGACACCCTCCGCCTTCAATACGGGAGCTGGGAGGCGGAGCTAGGGAAGAAGCTCGACGCCACCCAGGGGGTGCTTGACGCTGCCGC[T/A]
GCCCGAGAACAGCGGGCGGCGGAGACCGAAGCGGCGTCCCGGCGGCGCGAAGAGGCCCTTGAGGCGCGCGCCATGGCGCTGGAAGAGCGCGCCTGCGTCG
CGACGCAGGCGCGCTCTTCCAGCGCCATGGCGCGCGCCTCAAGGGCCTCTTCGCGCCGCCGGGACGCCGCTTCGGTCTCCGCCGCCCGCTGTTCTCGGGC[A/T]
GCGGCAGCGTCAAGCACCCCCTGGGTGGCGTCGAGCTTCTTCCCTAGCTCCGCCTCCCAGCTCCCGTATTGAAGGCGGAGGGTGTCCTGCGCCTCGTTCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.40% | 0.30% | 6.22% | 93.10% | NA |
| All Indica | 2759 | 0.40% | 0.20% | 4.13% | 95.32% | NA |
| All Japonica | 1512 | 0.60% | 0.00% | 10.12% | 89.29% | NA |
| Aus | 269 | 0.00% | 2.20% | 5.95% | 91.82% | NA |
| Indica I | 595 | 0.00% | 0.00% | 1.51% | 98.49% | NA |
| Indica II | 465 | 0.60% | 0.00% | 7.53% | 91.83% | NA |
| Indica III | 913 | 0.30% | 0.10% | 4.38% | 95.18% | NA |
| Indica Intermediate | 786 | 0.50% | 0.50% | 3.82% | 95.17% | NA |
| Temperate Japonica | 767 | 0.70% | 0.00% | 7.30% | 92.05% | NA |
| Tropical Japonica | 504 | 0.80% | 0.00% | 15.28% | 83.93% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 8.30% | 91.70% | NA |
| VI/Aromatic | 96 | 0.00% | 2.10% | 3.12% | 94.79% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 8.89% | 91.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0602220624 | T -> A | LOC_Os06g05030.1 | synonymous_variant ; p.Ala719Ala; LOW | synonymous_codon | Average:19.045; most accessible tissue: Minghui63 root, score: 50.524 | N | N | N | N |
| vg0602220624 | T -> DEL | LOC_Os06g05030.1 | N | frameshift_variant | Average:19.045; most accessible tissue: Minghui63 root, score: 50.524 | N | N | N | N |