| Variant ID: vg1123253254 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 23253254 |
| Reference Allele: C | Alternative Allele: CTCGTCGGCTGATGCCAAGTGAAT,CTCGTCGGCTG,CAAGTGAAT |
| Primary Allele: C | Secondary Allele: CTCGTCGGCTGATGCCAAGT GAAT |
Inferred Ancestral Allele: Not determined.
CCTGCGCCAATAATGGCGCAACGGCGGCTGGCTTCTGCGGCTCGCCGGCGGCGGTGGCGGCCGCCGCCGCCGTCGTCTTCTTTGCCTCGTCGGCTGATGC[C/CTCGTCGGCTGATGCCAAGTGAAT,CTCGTCGGCTG,CAAGTGAAT]
ACCGCAGAGGCGTCCATGGATGATGGATCAGTATTCACTTGGAGTGCGTATGTCGACGAACTCGGTTGCTTGTGATCTGCTCGATCGATCGATCGATCTC
GAGATCGATCGATCGATCGAGCAGATCACAAGCAACCGAGTTCGTCGACATACGCACTCCAAGTGAATACTGATCCATCATCCATGGACGCCTCTGCGGT[G/ATTCACTTGGCATCAGCCGACGAG,CAGCCGACGAG,ATTCACTTG]
GCATCAGCCGACGAGGCAAAGAAGACGACGGCGGCGGCGGCCGCCACCGCCGCCGGCGAGCCGCAGAAGCCAGCCGCCGTTGCGCCATTATTGGCGCAGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CTCGTCGGCTGATGCCAAGT GAAT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.10% | 2.70% | 0.13% | 0.00% | CTCGTCGGCTG: 0.06%; CAAGTGAAT: 0.02% |
| All Indica | 2759 | 99.50% | 0.50% | 0.04% | 0.00% | CAAGTGAAT: 0.04% |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 58.70% | 38.30% | 1.86% | 0.00% | CTCGTCGGCTG: 1.12% |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.40% | 0.00% | 0.00% | CAAGTGAAT: 0.22% |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 1.10% | 0.13% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1123253254 | C -> CTCGTCGGCTGATGCCAAGTGAAT | LOC_Os11g39060.1 | frameshift_variant ; p.Ala7fs; HIGH | frameshift_variant | Average:68.695; most accessible tissue: Callus, score: 82.581 | N | N | N | N |
| vg1123253254 | C -> CAAGTGAAT | LOC_Os11g39060.1 | frameshift_variant ; p.Ala7fs; HIGH | frameshift_variant | Average:68.695; most accessible tissue: Callus, score: 82.581 | N | N | N | N |
| vg1123253254 | C -> CTCGTCGGCTG | LOC_Os11g39060.1 | frameshift_variant ; p.Ala7fs; HIGH | frameshift_variant | Average:68.695; most accessible tissue: Callus, score: 82.581 | N | N | N | N |