| Variant ID: vg1117778679 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 17778679 |
| Reference Allele: CA | Alternative Allele: C |
| Primary Allele: CA | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AAGGTTGATGAACGCATGGCCGCACATCGGTCCCATGATCCCCAGCCGACCATTCCTCCTGCAATGGTGAGCCCGTCAGGAAACCGTAGCAGCTGCGCCT[CA/C]
ACGGGGCAGGTAGGATCACAGAGCATGGACGTCATGCAAACACAGGACGAATCGACCTGTCCTGTTGATGACATCACTCAGCGGACACCATGTGAGCTGC
GCAGCTCACATGGTGTCCGCTGAGTGATGTCATCAACAGGACAGGTCGATTCGTCCTGTGTTTGCATGACGTCCATGCTCTGTGATCCTACCTGCCCCGT[TG/G]
AGGCGCAGCTGCTACGGTTTCCTGACGGGCTCACCATTGCAGGAGGAATGGTCGGCTGGGGATCATGGGACCGATGTGCGGCCATGCGTTCATCAACCTT
| Populations | Population Size | Frequency of CA(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 24.20% | 0.20% | 1.78% | 73.87% | NA |
| All Indica | 2759 | 8.20% | 0.30% | 1.23% | 90.32% | NA |
| All Japonica | 1512 | 54.40% | 0.00% | 1.32% | 44.31% | NA |
| Aus | 269 | 9.30% | 0.00% | 8.18% | 82.53% | NA |
| Indica I | 595 | 7.20% | 0.00% | 0.50% | 92.27% | NA |
| Indica II | 465 | 22.80% | 0.00% | 1.29% | 75.91% | NA |
| Indica III | 913 | 2.00% | 0.70% | 1.86% | 95.51% | NA |
| Indica Intermediate | 786 | 7.40% | 0.30% | 1.02% | 91.35% | NA |
| Temperate Japonica | 767 | 63.20% | 0.00% | 1.43% | 35.33% | NA |
| Tropical Japonica | 504 | 27.80% | 0.00% | 1.79% | 70.44% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 0.00% | 18.26% | NA |
| VI/Aromatic | 96 | 49.00% | 0.00% | 2.08% | 48.96% | NA |
| Intermediate | 90 | 26.70% | 0.00% | 6.67% | 66.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117778679 | CA -> DEL | LOC_Os11g30552.1 | N | frameshift_variant | Average:5.695; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg1117778679 | CA -> C | LOC_Os11g30552.1 | frameshift_variant ; p.Thr545fs; HIGH | frameshift_variant | Average:5.695; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |