| Variant ID: vg1111258296 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 11258296 |
| Reference Allele: CTG | Alternative Allele: C |
| Primary Allele: CTG | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TAATCAATTGACAAACAAATCATTCTTCAAGATCAGGATGCACATCAGTCTTGCCATCTGCAGGAAGAGGGAAAGCAGAAGAGCCAGGCATGGCTTGTGA[CTG/C]
TGGAGAAGCAAGCCAAGCAGTCGGTGGCAGTGAGAACCAGAGACCTCCATATGGATACGGCGCTGCCTGCGGCGTCGGAACAGCGAGAGGACCAGTAGAT
ATCTACTGGTCCTCTCGCTGTTCCGACGCCGCAGGCAGCGCCGTATCCATATGGAGGTCTCTGGTTCTCACTGCCACCGACTGCTTGGCTTGCTTCTCCA[CAG/G]
TCACAAGCCATGCCTGGCTCTTCTGCTTTCCCTCTTCCTGCAGATGGCAAGACTGATGTGCATCCTGATCTTGAAGAATGATTTGTTTGTCAATTGATTA
| 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 | 90.20% | 0.10% | 0.21% | 9.52% | NA |
| All Indica | 2759 | 84.10% | 0.00% | 0.33% | 15.59% | NA |
| All Japonica | 1512 | 99.10% | 0.10% | 0.00% | 0.79% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 79.70% | 0.00% | 0.17% | 20.17% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.00% | 0.43% | NA |
| Indica III | 913 | 75.50% | 0.00% | 0.77% | 23.77% | NA |
| Indica Intermediate | 786 | 88.30% | 0.00% | 0.13% | 11.58% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 98.80% | 0.40% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 2.20% | 1.11% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1111258296 | CTG -> DEL | LOC_Os11g19530.1 | N | frameshift_variant | Average:73.147; most accessible tissue: Zhenshan97 panicle, score: 88.625 | N | N | N | N |
| vg1111258296 | CTG -> C | LOC_Os11g19530.1 | N | frameshift_variant | Average:73.147; most accessible tissue: Zhenshan97 panicle, score: 88.625 | N | N | N | N |