| Variant ID: vg1105161006 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5161006 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TAGACGAGGAGGCGACGCTCCCCACCTCGCCGCCCTTCCCCATCACCCGTGGATGTCGAAGTCGCGGATCCTTCGACCCTCTCGAGCGCCTCCTCCCGCC[T/G]
AGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTTGGCTCCCCGTCGTCACCGCTAACACTCGGAGAGAGGTTGTGCGCCTTT
AAAGGCGCACAACCTCTCTCCGAGTGTTAGCGGTGACGACGGGGAGCCAAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCT[A/C]
GGCGGGAGGAGGCGCTCGAGAGGGTCGAAGGATCCGCGACTTCGACATCCACGGGTGATGGGGAAGGGCGGCGAGGTGGGGAGCGTCGCCTCCTCGTCTA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.50% | 0.20% | 13.86% | 25.41% | NA |
| All Indica | 2759 | 44.10% | 0.40% | 18.92% | 36.61% | NA |
| All Japonica | 1512 | 90.90% | 0.00% | 1.46% | 7.61% | NA |
| Aus | 269 | 48.70% | 0.00% | 33.83% | 17.47% | NA |
| Indica I | 595 | 29.90% | 0.20% | 15.13% | 54.79% | NA |
| Indica II | 465 | 34.60% | 0.60% | 18.28% | 46.45% | NA |
| Indica III | 913 | 55.30% | 0.40% | 24.10% | 20.15% | NA |
| Indica Intermediate | 786 | 47.30% | 0.40% | 16.16% | 36.13% | NA |
| Temperate Japonica | 767 | 90.90% | 0.00% | 0.39% | 8.74% | NA |
| Tropical Japonica | 504 | 94.80% | 0.00% | 0.40% | 4.76% | NA |
| Japonica Intermediate | 241 | 83.00% | 0.00% | 7.05% | 9.96% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 9.38% | 7.29% | NA |
| Intermediate | 90 | 63.30% | 0.00% | 12.22% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105161006 | T -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:6.767; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1105161006 | T -> G | LOC_Os11g09660.1 | synonymous_variant ; p.Arg39Arg; LOW | synonymous_codon | Average:6.767; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |