| Variant ID: vg1012223917 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12223917 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AAAAAAAAAAATATCAGGGAGCAGCCGCCGCCGACGAGGTTGTCCACGGCAAGGGAGCGGGTAGCGGCGACCGCGCGCCAGGAGCGACCAATGGCGCGGA[T/G]
GCGGACACGGTCGGGGAGGGAGCGCGAGGACGGCGGCGTGGAGCGTGAGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAGCGCGAGCAG
CTGCTCGCGCTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCTCACGCTCCACGCCGCCGTCCTCGCGCTCCCTCCCCGACCGTGTCCGC[A/C]
TCCGCGCCATTGGTCGCTCCTGGCGCGCGGTCGCCGCTACCCGCTCCCTTGCCGTGGACAACCTCGTCGGCGGCGGCTGCTCCCTGATATTTTTTTTTTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.70% | 0.20% | 0.87% | 49.30% | NA |
| All Indica | 2759 | 33.20% | 0.10% | 0.94% | 65.71% | NA |
| All Japonica | 1512 | 88.50% | 0.10% | 0.20% | 11.24% | NA |
| Aus | 269 | 10.00% | 1.10% | 3.72% | 85.13% | NA |
| Indica I | 595 | 14.50% | 0.20% | 0.84% | 84.54% | NA |
| Indica II | 465 | 41.70% | 0.00% | 1.29% | 56.99% | NA |
| Indica III | 913 | 36.70% | 0.20% | 0.77% | 62.32% | NA |
| Indica Intermediate | 786 | 38.40% | 0.00% | 1.02% | 60.56% | NA |
| Temperate Japonica | 767 | 95.70% | 0.00% | 0.00% | 4.30% | NA |
| Tropical Japonica | 504 | 81.70% | 0.00% | 0.20% | 18.06% | NA |
| Japonica Intermediate | 241 | 79.70% | 0.40% | 0.83% | 19.09% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 2.08% | 88.54% | NA |
| Intermediate | 90 | 62.20% | 1.10% | 0.00% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012223917 | T -> G | LOC_Os10g23830.1 | missense_variant ; p.Met4Arg; MODERATE | nonsynonymous_codon ; M4R | Average:8.866; most accessible tissue: Callus, score: 26.513 | unknown | unknown | TOLERATED | 1.00 |
| vg1012223917 | T -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:8.866; most accessible tissue: Callus, score: 26.513 | N | N | N | N |