| Variant ID: vg0811599573 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599573 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGGCCGCCCCGCCGCTGTGCGCTCTCGCGTCCAGCTCCTTCGCCCGCGCCTCGAGCTCAGCGGCCCGCTGATCCAGTGCGGCCCTCTCGGCGCGGACGCC[T/A]
TCCAGATTGCGGCGCGCCTGCTCCTCCCGCGCTGCCTCGCGGAGGAACAGGCTGTCCGCCAGCCGCTGCGCCGCGGCCTCGGCCTCCTCAGCCTGGTGAA
TTCACCAGGCTGAGGAGGCCGAGGCCGCGGCGCAGCGGCTGGCGGACAGCCTGTTCCTCCGCGAGGCAGCGCGGGAGGAGCAGGCGCGCCGCAATCTGGA[A/T]
GGCGTCCGCGCCGAGAGGGCCGCACTGGATCAGCGGGCCGCTGAGCTCGAGGCGCGGGCGAAGGAGCTGGACGCGAGAGCGCACAGCGGCGGGGCGGCCG
| 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 | 3.00% | 0.20% | 2.54% | 94.18% | NA |
| All Indica | 2759 | 1.10% | 0.40% | 3.41% | 95.07% | NA |
| All Japonica | 1512 | 6.30% | 0.00% | 0.66% | 93.06% | NA |
| Aus | 269 | 4.10% | 0.00% | 4.83% | 91.08% | NA |
| Indica I | 595 | 0.70% | 0.20% | 0.67% | 98.49% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.43% | 99.57% | NA |
| Indica III | 913 | 2.00% | 1.00% | 7.56% | 89.49% | NA |
| Indica Intermediate | 786 | 1.10% | 0.10% | 2.42% | 96.31% | NA |
| Temperate Japonica | 767 | 7.80% | 0.00% | 0.52% | 91.66% | NA |
| Tropical Japonica | 504 | 4.80% | 0.00% | 0.60% | 94.64% | NA |
| Japonica Intermediate | 241 | 4.60% | 0.00% | 1.24% | 94.19% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 2.08% | 93.75% | NA |
| Intermediate | 90 | 3.30% | 0.00% | 1.11% | 95.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599573 | T -> A | LOC_Os08g19400.1 | missense_variant ; p.Glu110Asp; MODERATE | nonsynonymous_codon ; E110D | Average:16.881; most accessible tissue: Zhenshan97 root, score: 29.203 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0811599573 | T -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:16.881; most accessible tissue: Zhenshan97 root, score: 29.203 | N | N | N | N |