| Variant ID: vg0811599216 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599216 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGGCCTGGTAGCTTGCCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGGGAGCCGCTTGAG[G/A]
GTCCCGGCCATCTCTGAGAGGCGCTGGGCGAGGCCCCCCTGGTTGGCGGCGTACTTCGCGTACCGCCCGCCCCAGAGGCCCGCCTGCCGCCCGGCACGGT
ACCGTGCCGGGCGGCAGGCGGGCCTCTGGGGCGGGCGGTACGCGAAGTACGCCGCCAACCAGGGGGGCCTCGCCCAGCGCCTCTCAGAGATGGCCGGGAC[C/T]
CTCAAGCGGCTCCCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGGCAAGCTACCAGGCCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.70% | 2.30% | 4.89% | 49.13% | NA |
| All Indica | 2759 | 53.20% | 0.40% | 2.28% | 44.11% | NA |
| All Japonica | 1512 | 26.10% | 5.40% | 9.99% | 58.53% | NA |
| Aus | 269 | 48.30% | 3.30% | 2.23% | 46.10% | NA |
| Indica I | 595 | 32.60% | 0.00% | 3.87% | 63.53% | NA |
| Indica II | 465 | 36.60% | 0.20% | 2.37% | 60.86% | NA |
| Indica III | 913 | 77.00% | 0.90% | 1.64% | 20.48% | NA |
| Indica Intermediate | 786 | 50.90% | 0.40% | 1.78% | 46.95% | NA |
| Temperate Japonica | 767 | 16.90% | 2.90% | 13.17% | 67.01% | NA |
| Tropical Japonica | 504 | 37.50% | 8.90% | 6.55% | 47.02% | NA |
| Japonica Intermediate | 241 | 31.50% | 5.80% | 7.05% | 55.60% | NA |
| VI/Aromatic | 96 | 41.70% | 2.10% | 7.29% | 48.96% | NA |
| Intermediate | 90 | 36.70% | 4.40% | 4.44% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599216 | G -> A | LOC_Os08g19400.1 | synonymous_variant ; p.Thr229Thr; LOW | synonymous_codon | Average:21.265; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |
| vg0811599216 | G -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:21.265; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |