| Variant ID: vg1201734981 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 1734981 |
| Reference Allele: GACACAGCC | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: GACACAGCC |
Inferred Ancestral Allele: Not determined.
CGGGTGAGCGCCACCTGCCCGGTGTGCCGCGACTCGCCGCTGCCGTCGCCGATGGCCACGCCGCTCGCGGAGGCCGTGCCCCTCGCTGCGCACGCTCGAT[GACACAGCC/G]
ACACAGGTTCACATGTCACATATGTTACTGTGCTCTGTAGACAATTTTTGCTCTCTCGAATTTTCTTTGCTTCATTCGAAGCGTGAATGCGTGATTGATG
CATCAATCACGCATTCACGCTTCGAATGAAGCAAAGAAAATTCGAGAGAGCAAAAATTGTCTACAGAGCACAGTAACATATGTGACATGTGAACCTGTGT[GGCTGTGTC/C]
ATCGAGCGTGCGCAGCGAGGGGCACGGCCTCCGCGAGCGGCGTGGCCATCGGCGACGGCAGCGGCGAGTCGCGGCACACCGGGCAGGTGGCGCTCACCCG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GACACAGCC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 44.60% | 44.30% | 5.97% | 5.12% | NA |
| All Indica | 2759 | 73.30% | 8.80% | 9.82% | 8.12% | NA |
| All Japonica | 1512 | 1.30% | 97.40% | 0.53% | 0.86% | NA |
| Aus | 269 | 16.40% | 83.30% | 0.37% | 0.00% | NA |
| Indica I | 595 | 76.10% | 4.20% | 13.61% | 6.05% | NA |
| Indica II | 465 | 62.60% | 6.00% | 11.18% | 20.22% | NA |
| Indica III | 913 | 79.80% | 10.10% | 6.68% | 3.40% | NA |
| Indica Intermediate | 786 | 69.80% | 12.30% | 9.80% | 8.02% | NA |
| Temperate Japonica | 767 | 1.60% | 95.80% | 0.91% | 1.69% | NA |
| Tropical Japonica | 504 | 1.00% | 98.80% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 3.10% | 96.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 23.30% | 68.90% | 2.22% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1201734981 | GACACAGCC -> DEL | LOC_Os12g04130.1 | N | frameshift_variant | Average:54.47; most accessible tissue: Callus, score: 97.001 | N | N | N | N |
| vg1201734981 | GACACAGCC -> G | LOC_Os12g04130.1 | frameshift_variant&stop_lost&splice_region_variant ; p.Ter677fs; HIGH | frameshift_variant | Average:54.47; most accessible tissue: Callus, score: 97.001 | N | N | N | N |
| vg1201734981 | GACACAGCC -> G | LOC_Os12g04130.1 | downstream_gene_variant ; 0.0bp to feature; MODIFIER | frameshift_variant | Average:54.47; most accessible tissue: Callus, score: 97.001 | N | N | N | N |