| Variant ID: vg0811599219 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599219 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCTGGTAGCTTGCCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGGGAGCCGCTTGAGGGT[C/T]
CCGGCCATCTCTGAGAGGCGCTGGGCGAGGCCCCCCTGGTTGGCGGCGTACTTCGCGTACCGCCCGCCCCAGAGGCCCGCCTGCCGCCCGGCACGGTCTA
TAGACCGTGCCGGGCGGCAGGCGGGCCTCTGGGGCGGGCGGTACGCGAAGTACGCCGCCAACCAGGGGGGCCTCGCCCAGCGCCTCTCAGAGATGGCCGG[G/A]
ACCCTCAAGCGGCTCCCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGGCAAGCTACCAGG
| 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 | 47.60% | 0.40% | 2.77% | 49.17% | NA |
| All Indica | 2759 | 53.40% | 0.30% | 2.03% | 44.26% | NA |
| All Japonica | 1512 | 36.40% | 0.70% | 4.56% | 58.40% | NA |
| Aus | 269 | 52.80% | 0.70% | 0.37% | 46.10% | NA |
| Indica I | 595 | 32.60% | 0.00% | 3.87% | 63.53% | NA |
| Indica II | 465 | 36.60% | 0.00% | 2.15% | 61.29% | NA |
| Indica III | 913 | 77.50% | 0.50% | 1.20% | 20.70% | NA |
| Indica Intermediate | 786 | 51.10% | 0.40% | 1.53% | 46.95% | NA |
| Temperate Japonica | 767 | 27.50% | 0.10% | 5.74% | 66.62% | NA |
| Tropical Japonica | 504 | 48.00% | 1.00% | 3.77% | 47.22% | NA |
| Japonica Intermediate | 241 | 40.20% | 1.70% | 2.49% | 55.60% | NA |
| VI/Aromatic | 96 | 49.00% | 0.00% | 2.08% | 48.96% | NA |
| Intermediate | 90 | 42.20% | 0.00% | 3.33% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599219 | C -> T | LOC_Os08g19400.1 | synonymous_variant ; p.Gly228Gly; LOW | synonymous_codon | Average:21.193; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |
| vg0811599219 | C -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:21.193; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |