| Variant ID: vg1123253256 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 23253256 |
| Reference Allele: C | Alternative Allele: CTGATCCATCATCCATGGA,CTGATCCATCATCCATGGACGCCTCGT |
| Primary Allele: C | Secondary Allele: CTGATCCATCATCCATGGA |
Inferred Ancestral Allele: Not determined.
TGCGCCAATAATGGCGCAACGGCGGCTGGCTTCTGCGGCTCGCCGGCGGCGGTGGCGGCCGCCGCCGCCGTCGTCTTCTTTGCCTCGTCGGCTGATGCCA[C/CTGATCCATCATCCATGGA,CTGATCCATCATCCATGGACGCCTCGT]
CGCAGAGGCGTCCATGGATGATGGATCAGTATTCACTTGGAGTGCGTATGTCGACGAACTCGGTTGCTTGTGATCTGCTCGATCGATCGATCGATCTCAC
GTGAGATCGATCGATCGATCGAGCAGATCACAAGCAACCGAGTTCGTCGACATACGCACTCCAAGTGAATACTGATCCATCATCCATGGACGCCTCTGCG[G/TCCATGGATGATGGATCAG,ACGAGGCGTCCATGGATGATGGATCAG]
TGGCATCAGCCGACGAGGCAAAGAAGACGACGGCGGCGGCGGCCGCCACCGCCGCCGGCGAGCCGCAGAAGCCAGCCGCCGTTGCGCCATTATTGGCGCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CTGATCCATCATCCATGGA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.10% | 2.80% | 0.06% | 0.00% | CTGATCCATCATCCATGGACGCCTCGT: 0.02% |
| All Indica | 2759 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 58.40% | 40.10% | 1.12% | 0.00% | CTGATCCATCATCCATGGACGCCTCGT: 0.37% |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1123253256 | C -> CTGATCCATCATCCATGGACGCCTCGT | LOC_Os11g39060.1 | frameshift_variant ; p.Val6fs; HIGH | frameshift_variant | Average:68.634; most accessible tissue: Callus, score: 82.581 | N | N | N | N |
| vg1123253256 | C -> CTGATCCATCATCCATGGA | LOC_Os11g39060.1 | inframe_insertion ; p.Ala5_Val6insSerMetAspAspGlyS er; MODERATE | inframe_variant | Average:68.634; most accessible tissue: Callus, score: 82.581 | N | N | N | N |