| Variant ID: vg0620132090 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20132090 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGCGGCTGCCGGCGTGCAAGCACCTGTACCACGTGGAGTGCATCGACATGTGGCTGGCCTCGCACGCCACGTGCCCAATCTGCCGGACGGAGGTCGAGCC[A/G]
CCGCCGGAGGACGACGACGGCCGACCTGCGCCGGCGGCAGATGAGTCGTCGCCGACGGAGGCGCTGCCACCGGTGTAGCTAGTTCTGTGCTAGCTAACTA
TAGTTAGCTAGCACAGAACTAGCTACACCGGTGGCAGCGCCTCCGTCGGCGACGACTCATCTGCCGCCGGCGCAGGTCGGCCGTCGTCGTCCTCCGGCGG[T/C]
GGCTCGACCTCCGTCCGGCAGATTGGGCACGTGGCGTGCGAGGCCAGCCACATGTCGATGCACTCCACGTGGTACAGGTGCTTGCACGCCGGCAGCCGCC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 69.70% | 4.80% | 13.65% | 11.87% | NA |
| All Indica | 2759 | 75.20% | 0.20% | 12.40% | 12.25% | NA |
| All Japonica | 1512 | 54.30% | 12.20% | 19.51% | 13.96% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 65.40% | 0.00% | 25.04% | 9.58% | NA |
| Indica II | 465 | 63.70% | 0.60% | 13.76% | 21.94% | NA |
| Indica III | 913 | 87.30% | 0.10% | 3.07% | 9.53% | NA |
| Indica Intermediate | 786 | 75.30% | 0.10% | 12.85% | 11.70% | NA |
| Temperate Japonica | 767 | 50.20% | 4.60% | 26.60% | 18.64% | NA |
| Tropical Japonica | 504 | 67.70% | 14.50% | 10.71% | 7.14% | NA |
| Japonica Intermediate | 241 | 39.40% | 32.00% | 15.35% | 13.28% | NA |
| VI/Aromatic | 96 | 65.60% | 31.20% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 72.20% | 8.90% | 8.89% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620132090 | A -> G | LOC_Os06g34620.1 | synonymous_variant ; p.Pro149Pro; LOW | synonymous_codon | Average:66.359; most accessible tissue: Zhenshan97 panicle, score: 81.752 | N | N | N | N |
| vg0620132090 | A -> DEL | LOC_Os06g34620.1 | N | frameshift_variant | Average:66.359; most accessible tissue: Zhenshan97 panicle, score: 81.752 | N | N | N | N |