| Variant ID: vg0131447850 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31447850 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCCGGATGGATGACCTCACGGATGAATCCGGCTTCCAGAAGTCGCGCCACCTCCTCGCGGATGAAGGCTTGACGTTCCGGGGCCTGCCGCCGCACTTTCT[G/A]
CCGGACCGGCCTTGCGCCCGGCCGCACGGCGAGACGGTGCTCAATCACCTCCCTGGGGACCCCGGGCATATCCGCCGGTCTCCATGCGAAGACGTCAGCG
CGCTGACGTCTTCGCATGGAGACCGGCGGATATGCCCGGGGTCCCCAGGGAGGTGATTGAGCACCGTCTCGCCGTGCGGCCGGGCGCAAGGCCGGTCCGG[C/T]
AGAAAGTGCGGCGGCAGGCCCCGGAACGTCAAGCCTTCATCCGCGAGGAGGTGGCGCGACTTCTGGAAGCCGGATTCATCCGTGAGGTCATCCATCCGGA
| 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 | 51.60% | 0.80% | 3.41% | 44.16% | NA |
| All Indica | 2759 | 42.70% | 1.40% | 5.33% | 50.60% | NA |
| All Japonica | 1512 | 69.00% | 0.00% | 0.46% | 30.49% | NA |
| Aus | 269 | 25.70% | 0.00% | 1.12% | 73.23% | NA |
| Indica I | 595 | 30.80% | 0.80% | 4.71% | 63.70% | NA |
| Indica II | 465 | 30.30% | 0.40% | 3.87% | 65.38% | NA |
| Indica III | 913 | 56.30% | 3.20% | 6.68% | 33.84% | NA |
| Indica Intermediate | 786 | 43.10% | 0.40% | 5.09% | 51.40% | NA |
| Temperate Japonica | 767 | 59.80% | 0.00% | 0.39% | 39.77% | NA |
| Tropical Japonica | 504 | 91.10% | 0.00% | 0.20% | 8.73% | NA |
| Japonica Intermediate | 241 | 52.30% | 0.00% | 1.24% | 46.47% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 1.04% | 4.17% | NA |
| Intermediate | 90 | 64.40% | 0.00% | 3.33% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131447850 | G -> A | LOC_Os01g54660.1 | stop_gained ; p.Gln829*; HIGH | stop_gained | Average:24.244; most accessible tissue: Zhenshan97 panicle, score: 54.901 | N | N | N | N |
| vg0131447850 | G -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:24.244; most accessible tissue: Zhenshan97 panicle, score: 54.901 | N | N | N | N |