| Variant ID: vg0721993506 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 21993506 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 345. )
CCCCCTCAAGATGGGCGATAAATATCTATCATGCCCATCTTGCTACACGAAGAAGTGCACTCTCTAGCACCTAATGCCTTCGTTAAACTATCAGCTACTT[G/A]
TTCACCAGAGTTTACAAAGCCTAAGTTTAAGGTTCCCTCATCCATTCTCTCTTTAATAAAGAAGCGATCTATTTCCACATGCTTCGTTCGATCATGCTGG
CCAGCATGATCGAACGAAGCATGTGGAAATAGATCGCTTCTTTATTAAAGAGAGAATGGATGAGGGAACCTTAAACTTAGGCTTTGTAAACTCTGGTGAA[C/T]
AAGTAGCTGATAGTTTAACGAAGGCATTAGGTGCTAGAGAGTGCACTTCTTCGTGTAGCAAGATGGGCATGATAGATATTTATCGCCCATCTTGAGGGGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.00% | 0.00% | 3.36% | 8.65% | NA |
| All Indica | 2759 | 84.50% | 0.00% | 4.93% | 10.55% | NA |
| All Japonica | 1512 | 92.40% | 0.00% | 0.13% | 7.47% | NA |
| Aus | 269 | 92.20% | 0.00% | 7.06% | 0.74% | NA |
| Indica I | 595 | 49.70% | 0.00% | 16.47% | 33.78% | NA |
| Indica II | 465 | 94.60% | 0.00% | 1.08% | 4.30% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 86.80% | 0.10% | 4.20% | 8.91% | NA |
| Temperate Japonica | 767 | 97.00% | 0.00% | 0.00% | 3.00% | NA |
| Tropical Japonica | 504 | 89.70% | 0.00% | 0.20% | 10.12% | NA |
| Japonica Intermediate | 241 | 83.40% | 0.00% | 0.41% | 16.18% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 0.00% | 2.22% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0721993506 | G -> DEL | LOC_Os07g36710.1 | N | frameshift_variant | Average:7.197; most accessible tissue: Callus, score: 32.482 | N | N | N | N |
| vg0721993506 | G -> A | LOC_Os07g36710.1 | stop_gained ; p.Gln773*; HIGH | stop_gained | Average:7.197; most accessible tissue: Callus, score: 32.482 | N | N | N | N |