| Variant ID: vg0811599533 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599533 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCGGCGGCTGCGAGGCGGGCGGCTAGGTCGCCCTGGCCCGCGGCCGCCCCGCCGCTGTGCGCTCTCGCGTCCAGCTCCTTCGCCCGCGCCTCGAGCTCAG[C/T]
GGCCCGCTGATCCAGTGCGGCCCTCTCGGCGCGGACGCCTTCCAGATTGCGGCGCGCCTGCTCCTCCCGCGCTGCCTCGCGGAGGAACAGGCTGTCCGCC
GGCGGACAGCCTGTTCCTCCGCGAGGCAGCGCGGGAGGAGCAGGCGCGCCGCAATCTGGAAGGCGTCCGCGCCGAGAGGGCCGCACTGGATCAGCGGGCC[G/A]
CTGAGCTCGAGGCGCGGGCGAAGGAGCTGGACGCGAGAGCGCACAGCGGCGGGGCGGCCGCGGGCCAGGGCGACCTAGCCGCCCGCCTCGCAGCCGCCGA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 1.00% | 0.60% | 4.15% | 94.22% | NA |
| All Indica | 2759 | 1.70% | 0.70% | 3.04% | 94.64% | NA |
| All Japonica | 1512 | 0.00% | 0.40% | 6.02% | 93.58% | NA |
| Aus | 269 | 0.40% | 1.50% | 5.95% | 92.19% | NA |
| Indica I | 595 | 0.50% | 0.70% | 1.01% | 97.82% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.43% | 99.57% | NA |
| Indica III | 913 | 3.50% | 0.90% | 7.12% | 88.50% | NA |
| Indica Intermediate | 786 | 1.40% | 0.80% | 1.40% | 96.44% | NA |
| Temperate Japonica | 767 | 0.00% | 0.40% | 7.43% | 92.18% | NA |
| Tropical Japonica | 504 | 0.00% | 0.20% | 4.56% | 95.24% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.80% | 4.56% | 94.61% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 2.08% | 96.88% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 3.33% | 95.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599533 | C -> T | LOC_Os08g19400.1 | missense_variant ; p.Ala124Thr; MODERATE | nonsynonymous_codon ; A124T | Average:16.662; most accessible tissue: Zhenshan97 root, score: 29.203 | unknown | unknown | DELETERIOUS | 0.02 |
| vg0811599533 | C -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:16.662; most accessible tissue: Zhenshan97 root, score: 29.203 | N | N | N | N |