| Variant ID: vg1105160032 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 5160032 |
| Reference Allele: AC | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: AC |
Inferred Ancestral Allele: Not determined.
CCTCTTCCTTACGAGCCACTCGGTCCGCGAGCTGAAAAAGCTCCGCGGTAGTCTGGAGCTCTTTGGAGGCGATCTTTTCGATCATGCGGTTGTGCCGCAC[AC/A]
CCCCCCTGAACGCGTAGATCACCGCGTGTGCAGGGATGCATGGTATGGTGTTGCAGACTTGACAGAACCGCTGAATGTATGAGCGAAGTGACTCATCATC
GATGATGAGTCACTTCGCTCATACATTCAGCGGTTCTGTCAAGTCTGCAACACCATACCATGCATCCCTGCACACGCGGTGATCTACGCGTTCAGGGGGG[GT/T]
GTGCGGCACAACCGCATGATCGAAAAGATCGCCTCCAAAGAGCTCCAGACTACCGCGGAGCTTTTTCAGCTCGCGGACCGAGTGGCTCGTAAGGAAGAGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 22.20% | 10.60% | 3.85% | 63.27% | NA |
| All Indica | 2759 | 8.30% | 1.10% | 5.40% | 85.21% | NA |
| All Japonica | 1512 | 53.00% | 29.80% | 0.79% | 16.40% | NA |
| Aus | 269 | 0.00% | 1.50% | 2.23% | 96.28% | NA |
| Indica I | 595 | 2.90% | 2.50% | 3.19% | 91.43% | NA |
| Indica II | 465 | 3.70% | 1.10% | 1.72% | 93.55% | NA |
| Indica III | 913 | 7.20% | 0.20% | 9.31% | 83.24% | NA |
| Indica Intermediate | 786 | 16.40% | 1.00% | 4.71% | 77.86% | NA |
| Temperate Japonica | 767 | 52.90% | 34.90% | 0.39% | 11.73% | NA |
| Tropical Japonica | 504 | 63.30% | 14.50% | 1.79% | 20.44% | NA |
| Japonica Intermediate | 241 | 32.00% | 45.20% | 0.00% | 22.82% | NA |
| VI/Aromatic | 96 | 2.10% | 5.20% | 12.50% | 80.21% | NA |
| Intermediate | 90 | 20.00% | 15.60% | 3.33% | 61.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105160032 | AC -> A | LOC_Os11g09660.1 | frameshift_variant ; p.Gly363fs; HIGH | frameshift_variant | Average:6.36; most accessible tissue: Callus, score: 13.429 | N | N | N | N |
| vg1105160032 | AC -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:6.36; most accessible tissue: Callus, score: 13.429 | N | N | N | N |