| Variant ID: vg0811599213 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599213 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCCTGGCCTGGTAGCTTGCCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGGGAGCCGCTT[G/C]
AGGGTCCCGGCCATCTCTGAGAGGCGCTGGGCGAGGCCCCCCTGGTTGGCGGCGTACTTCGCGTACCGCCCGCCCCAGAGGCCCGCCTGCCGCCCGGCAC
GTGCCGGGCGGCAGGCGGGCCTCTGGGGCGGGCGGTACGCGAAGTACGCCGCCAACCAGGGGGGCCTCGCCCAGCGCCTCTCAGAGATGGCCGGGACCCT[C/G]
AAGCGGCTCCCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGGCAAGCTACCAGGCCAGGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.50% | 0.00% | 2.45% | 48.98% | NA |
| All Indica | 2759 | 53.90% | 0.00% | 1.96% | 44.11% | NA |
| All Japonica | 1512 | 38.00% | 0.10% | 3.84% | 58.07% | NA |
| Aus | 269 | 53.50% | 0.00% | 0.37% | 46.10% | NA |
| Indica I | 595 | 32.80% | 0.00% | 3.87% | 63.36% | NA |
| Indica II | 465 | 36.80% | 0.00% | 2.15% | 61.08% | NA |
| Indica III | 913 | 78.40% | 0.00% | 0.99% | 20.59% | NA |
| Indica Intermediate | 786 | 51.70% | 0.00% | 1.53% | 46.82% | NA |
| Temperate Japonica | 767 | 27.90% | 0.00% | 5.74% | 66.36% | NA |
| Tropical Japonica | 504 | 50.80% | 0.40% | 1.98% | 46.83% | NA |
| Japonica Intermediate | 241 | 43.20% | 0.00% | 1.66% | 55.19% | NA |
| VI/Aromatic | 96 | 51.00% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599213 | G -> C | LOC_Os08g19400.1 | synonymous_variant ; p.Leu230Leu; LOW | synonymous_codon | Average:21.61; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |
| vg0811599213 | G -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:21.61; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |