| Variant ID: vg0811599605 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599605 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGCTCCTTCGCCCGCGCCTCGAGCTCAGCGGCCCGCTGATCCAGTGCGGCCCTCTCGGCGCGGACGCCTTCCAGATTGCGGCGCGCCTGCTCCTCCCGCG[C/T]
TGCCTCGCGGAGGAACAGGCTGTCCGCCAGCCGCTGCGCCGCGGCCTCGGCCTCCTCAGCCTGGTGAACCCGGACGGCCTCCTGGGCAGCCTCCTCGGCT
AGCCGAGGAGGCTGCCCAGGAGGCCGTCCGGGTTCACCAGGCTGAGGAGGCCGAGGCCGCGGCGCAGCGGCTGGCGGACAGCCTGTTCCTCCGCGAGGCA[G/A]
CGCGGGAGGAGCAGGCGCGCCGCAATCTGGAAGGCGTCCGCGCCGAGAGGGCCGCACTGGATCAGCGGGCCGCTGAGCTCGAGGCGCGGGCGAAGGAGCT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.90% | 0.10% | 16.48% | 82.50% | NA |
| All Indica | 2759 | 0.90% | 0.10% | 14.68% | 84.31% | NA |
| All Japonica | 1512 | 0.90% | 0.00% | 15.67% | 83.40% | NA |
| Aus | 269 | 0.40% | 1.10% | 34.20% | 64.31% | NA |
| Indica I | 595 | 0.70% | 0.00% | 6.55% | 92.77% | NA |
| Indica II | 465 | 0.00% | 0.00% | 4.95% | 95.05% | NA |
| Indica III | 913 | 1.50% | 0.30% | 27.27% | 70.87% | NA |
| Indica Intermediate | 786 | 0.90% | 0.00% | 11.96% | 87.15% | NA |
| Temperate Japonica | 767 | 0.80% | 0.00% | 10.69% | 88.53% | NA |
| Tropical Japonica | 504 | 1.20% | 0.00% | 23.81% | 75.00% | NA |
| Japonica Intermediate | 241 | 0.80% | 0.00% | 14.52% | 84.65% | NA |
| VI/Aromatic | 96 | 1.00% | 1.00% | 31.25% | 66.67% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 16.67% | 83.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599605 | C -> T | LOC_Os08g19400.1 | missense_variant ; p.Ala100Thr; MODERATE | nonsynonymous_codon ; A100T | Average:16.861; most accessible tissue: Zhenshan97 root, score: 30.989 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0811599605 | C -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:16.861; most accessible tissue: Zhenshan97 root, score: 30.989 | N | N | N | N |