| Variant ID: vg0811599267 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599267 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGGGAGCCGCTTGAGGGTCCCGGCCATCTCTGAGAGGCGCTGGGCGAGGCCCCCCTGGTTGGCGGC[G/A]
TACTTCGCGTACCGCCCGCCCCAGAGGCCCGCCTGCCGCCCGGCACGGTCTAGACGGGAGACGGCATCCCGAAGCATGCCGGGCCCTACCTCGCTTGCCA
TGGCAAGCGAGGTAGGGCCCGGCATGCTTCGGGATGCCGTCTCCCGTCTAGACCGTGCCGGGCGGCAGGCGGGCCTCTGGGGCGGGCGGTACGCGAAGTA[C/T]
GCCGCCAACCAGGGGGGCCTCGCCCAGCGCCTCTCAGAGATGGCCGGGACCCTCAAGCGGCTCCCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGA
| 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 | 48.10% | 0.20% | 2.86% | 48.88% | NA |
| All Indica | 2759 | 53.00% | 0.30% | 2.65% | 44.04% | NA |
| All Japonica | 1512 | 38.20% | 0.10% | 3.84% | 57.87% | NA |
| Aus | 269 | 53.50% | 0.00% | 0.37% | 46.10% | NA |
| Indica I | 595 | 32.40% | 0.00% | 4.37% | 63.19% | NA |
| Indica II | 465 | 35.50% | 0.20% | 3.66% | 60.65% | NA |
| Indica III | 913 | 77.30% | 0.70% | 1.31% | 20.70% | NA |
| Indica Intermediate | 786 | 50.80% | 0.10% | 2.29% | 46.82% | NA |
| Temperate Japonica | 767 | 28.00% | 0.00% | 5.87% | 66.10% | NA |
| Tropical Japonica | 504 | 51.60% | 0.00% | 1.79% | 46.63% | NA |
| Japonica Intermediate | 241 | 42.70% | 0.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599267 | G -> A | LOC_Os08g19400.1 | synonymous_variant ; p.Tyr212Tyr; LOW | synonymous_codon | Average:20.351; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |
| vg0811599267 | G -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:20.351; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |