| Variant ID: vg1105161001 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5161001 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGCCGTAGACGAGGAGGCGACGCTCCCCACCTCGCCGCCCTTCCCCATCACCCGTGGATGTCGAAGTCGCGGATCCTTCGACCCTCTCGAGCGCCTCCTC[C/T]
CGCCTAGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTTGGCTCCCCGTCGTCACCGCTAACACTCGGAGAGAGGTTGTGCG
CGCACAACCTCTCTCCGAGTGTTAGCGGTGACGACGGGGAGCCAAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCTAGGCG[G/A]
GAGGAGGCGCTCGAGAGGGTCGAAGGATCCGCGACTTCGACATCCACGGGTGATGGGGAAGGGCGGCGAGGTGGGGAGCGTCGCCTCCTCGTCTACGGCG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.30% | 0.10% | 8.32% | 27.32% | NA |
| All Indica | 2759 | 50.50% | 0.10% | 12.21% | 37.19% | NA |
| All Japonica | 1512 | 90.90% | 0.00% | 1.39% | 7.74% | NA |
| Aus | 269 | 50.20% | 0.40% | 10.04% | 39.41% | NA |
| Indica I | 595 | 31.60% | 0.00% | 7.56% | 60.84% | NA |
| Indica II | 465 | 41.10% | 0.00% | 13.12% | 45.81% | NA |
| Indica III | 913 | 65.60% | 0.30% | 15.22% | 18.84% | NA |
| Indica Intermediate | 786 | 52.80% | 0.00% | 11.70% | 35.50% | NA |
| Temperate Japonica | 767 | 90.90% | 0.00% | 0.26% | 8.87% | NA |
| Tropical Japonica | 504 | 94.80% | 0.00% | 1.39% | 3.77% | NA |
| Japonica Intermediate | 241 | 82.60% | 0.00% | 4.98% | 12.45% | NA |
| VI/Aromatic | 96 | 80.20% | 0.00% | 1.04% | 18.75% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 7.78% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105161001 | C -> T | LOC_Os11g09660.1 | synonymous_variant ; p.Arg40Arg; LOW | synonymous_codon | Average:6.767; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1105161001 | C -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:6.767; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |