| Variant ID: vg1126903377 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 26903377 |
| Reference Allele: AGAG | Alternative Allele: A |
| Primary Allele: AGAG | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGTTTGGTTAAAGGGTAGGGTGGATGGGGCGGCCCGGAATAGAAAATATTCTCTTAATAGGCTGGACGACGAGTGATGTCCATGTGGCTGATAACGGGGA[AGAG/A]
GAGGAGGTAGGAGTCGATCCTGCTCTGAACATCCCTGAACTTTTCAGCCTGCCTCCCGGCCATCACCAACCTGTACATGGCGCTATTGTCCTGGCATGCC
GGCATGCCAGGACAATAGCGCCATGTACAGGTTGGTGATGGCCGGGAGGCAGGCTGAAAAGTTCAGGGATGTTCAGAGCAGGATCGACTCCTACCTCCTC[CTCT/T]
TCCCCGTTATCAGCCACATGGACATCACTCGTCGTCCAGCCTATTAAGAGAATATTTTCTATTCCGGGCCGCCCCATCCACCCTACCCTTTAACCAAACA
| Populations | Population Size | Frequency of AGAG(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 68.30% | 0.50% | 2.09% | 29.12% | NA |
| All Indica | 2759 | 60.70% | 0.00% | 1.52% | 37.73% | NA |
| All Japonica | 1512 | 78.70% | 1.50% | 3.24% | 16.53% | NA |
| Aus | 269 | 79.90% | 0.00% | 1.86% | 18.22% | NA |
| Indica I | 595 | 51.80% | 0.00% | 2.52% | 45.71% | NA |
| Indica II | 465 | 67.30% | 0.00% | 0.86% | 31.83% | NA |
| Indica III | 913 | 60.60% | 0.00% | 0.77% | 38.66% | NA |
| Indica Intermediate | 786 | 63.90% | 0.00% | 2.04% | 34.10% | NA |
| Temperate Japonica | 767 | 79.10% | 2.90% | 5.22% | 12.78% | NA |
| Tropical Japonica | 504 | 79.40% | 0.00% | 1.39% | 19.25% | NA |
| Japonica Intermediate | 241 | 75.90% | 0.40% | 0.83% | 22.82% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 1.04% | 9.38% | NA |
| Intermediate | 90 | 65.60% | 2.20% | 2.22% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126903377 | AGAG -> A | LOC_Os11g44460.1 | inframe_deletion ; p.Leu99del; MODERATE | inframe_variant | Average:13.198; most accessible tissue: Callus, score: 46.436 | N | N | N | N |
| vg1126903377 | AGAG -> DEL | LOC_Os11g44460.1 | N | frameshift_variant | Average:13.198; most accessible tissue: Callus, score: 46.436 | N | N | N | N |