| Variant ID: vg0811599476 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599476 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.02, others allele: 0.00, population size: 63. )
GCCTCGACCTCCCCGGCGGACGAGTCCAGTGCGCCCTGCGGCTCGGCGATGGTGTGTTCGGCGGCTGCGAGGCGGGCGGCTAGGTCGCCCTGGCCCGCGG[C/T]
CGCCCCGCCGCTGTGCGCTCTCGCGTCCAGCTCCTTCGCCCGCGCCTCGAGCTCAGCGGCCCGCTGATCCAGTGCGGCCCTCTCGGCGCGGACGCCTTCC
GGAAGGCGTCCGCGCCGAGAGGGCCGCACTGGATCAGCGGGCCGCTGAGCTCGAGGCGCGGGCGAAGGAGCTGGACGCGAGAGCGCACAGCGGCGGGGCG[G/A]
CCGCGGGCCAGGGCGACCTAGCCGCCCGCCTCGCAGCCGCCGAACACACCATCGCCGAGCCGCAGGGCGCACTGGACTCGTCCGCCGGGGAGGTCGAGGC
| 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 | 0.20% | 0.00% | 4.10% | 95.66% | NA |
| All Indica | 2759 | 0.40% | 0.00% | 3.62% | 96.01% | NA |
| All Japonica | 1512 | 0.00% | 0.10% | 5.42% | 94.51% | NA |
| Aus | 269 | 0.00% | 0.00% | 3.72% | 96.28% | NA |
| Indica I | 595 | 0.00% | 0.00% | 0.34% | 99.66% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.22% | 99.78% | NA |
| Indica III | 913 | 0.50% | 0.00% | 8.87% | 90.58% | NA |
| Indica Intermediate | 786 | 0.60% | 0.00% | 2.04% | 97.33% | NA |
| Temperate Japonica | 767 | 0.00% | 0.10% | 7.04% | 92.83% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 3.77% | 96.23% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 3.73% | 96.27% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 2.22% | 97.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599476 | C -> T | LOC_Os08g19400.1 | missense_variant ; p.Ala143Thr; MODERATE | nonsynonymous_codon ; A143T | Average:20.16; most accessible tissue: Zhenshan97 root, score: 32.766 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0811599476 | C -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:20.16; most accessible tissue: Zhenshan97 root, score: 32.766 | N | N | N | N |