| Variant ID: vg1105182879 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 5182879 |
| Reference Allele: CTG | Alternative Allele: C |
| Primary Allele: CTG | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTAGAGACTACGTTAGAAGCTGGATCTGCCCCGACTGTAGGAAGGAGTACAAGCCTATTCAAAACATGCTTGTTGATTTGCCGCCTTTCAGCTGTGATGA[CTG/C]
TGGGTTGAAGGTGAAATTTTTTCTCATCATCATTTTCTTCTAACCATGACTCTCTTTTCTTGTATTTTTTCTCCGCTAACCATATACCTCTCTTGTGTAG
CTACACAAGAGAGGTATATGGTTAGCGGAGAAAAAATACAAGAAAAGAGAGTCATGGTTAGAAGAAAATGATGATGAGAAAAAATTTCACCTTCAACCCA[CAG/G]
TCATCACAGCTGAAAGGCGGCAAATCAACAAGCATGTTTTGAATAGGCTTGTACTCCTTCCTACAGTCGGGGCAGATCCAGCTTCTAACGTAGTCTCTAG
| Populations | Population Size | Frequency of CTG(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 68.40% | 0.30% | 1.42% | 29.94% | NA |
| All Indica | 2759 | 51.30% | 0.00% | 2.10% | 46.57% | NA |
| All Japonica | 1512 | 97.90% | 0.80% | 0.20% | 1.12% | NA |
| Aus | 269 | 69.50% | 0.00% | 0.37% | 30.11% | NA |
| Indica I | 595 | 28.90% | 0.00% | 3.36% | 67.73% | NA |
| Indica II | 465 | 22.40% | 0.00% | 3.23% | 74.41% | NA |
| Indica III | 913 | 73.70% | 0.00% | 1.10% | 25.19% | NA |
| Indica Intermediate | 786 | 59.40% | 0.00% | 1.65% | 38.93% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 0.26% | 1.96% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 94.20% | 4.60% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 67.80% | 0.00% | 5.56% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105182879 | CTG -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:10.92; most accessible tissue: Callus, score: 56.21 | N | N | N | N |
| vg1105182879 | CTG -> C | LOC_Os11g09710.1 | frameshift_variant ; p.Cys73fs; HIGH | frameshift_variant | Average:10.92; most accessible tissue: Callus, score: 56.21 | N | N | N | N |