| Variant ID: vg0135357942 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35357942 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 286. )
CTGACTCATCCATATCATTTCTGATGCGTCTAGTTTGGCGTCGACCCTTTTTCACCCTTAACTTAGATGGATCTGGAATGTAAAAAACTTGGGCACTCAG[C/T]
GTTGTGTAAGATCCTGAGATCCCGAACCCATATATCTCCTCACTCCATGTATGAAAGATTGCTTCTTTCCTGAAATAATTTGAGACGTACACATTGGGAG
CTCCCAATGTGTACGTCTCAAATTATTTCAGGAAAGAAGCAATCTTTCATACATGGAGTGAGGAGATATATGGGTTCGGGATCTCAGGATCTTACACAAC[G/A]
CTGAGTGCCCAAGTTTTTTACATTCCAGATCCATCTAAGTTAAGGGTGAAAAAGGGTCGACGCCAAACTAGACGCATCAGAAATGATATGGATGAGTCAG
| 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 | 24.80% | 0.10% | 2.05% | 72.96% | NA |
| All Indica | 2759 | 2.40% | 0.10% | 1.41% | 96.09% | NA |
| All Japonica | 1512 | 64.40% | 0.10% | 3.24% | 32.34% | NA |
| Aus | 269 | 0.40% | 1.10% | 2.23% | 96.28% | NA |
| Indica I | 595 | 4.40% | 0.00% | 0.67% | 94.96% | NA |
| Indica II | 465 | 0.40% | 0.00% | 1.08% | 98.49% | NA |
| Indica III | 913 | 0.90% | 0.00% | 2.52% | 96.60% | NA |
| Indica Intermediate | 786 | 3.80% | 0.40% | 0.89% | 94.91% | NA |
| Temperate Japonica | 767 | 57.20% | 0.00% | 0.39% | 42.37% | NA |
| Tropical Japonica | 504 | 66.10% | 0.20% | 8.93% | 24.80% | NA |
| Japonica Intermediate | 241 | 83.40% | 0.00% | 0.41% | 16.18% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 50.00% | 0.00% | 3.33% | 46.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135357942 | C -> T | LOC_Os01g61090.1 | synonymous_variant ; p.Thr801Thr; LOW | synonymous_codon | Average:5.003; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |
| vg0135357942 | C -> DEL | LOC_Os01g61090.1 | N | frameshift_variant | Average:5.003; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |