| Variant ID: vg0727002572 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr07 | Position: 27002572 |
| Reference Allele: GT | Alternative Allele: G |
| Primary Allele: GT | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TTGCTCTGAAATCAAGCACTACAGAAGTTTGGTCAAAGCTGGGTATGGTGTTTACGCTCAAGTGGGGAAGGTTGCGGATCATGAATGCATGCCTACGGAG[GT/G]
TTTGCCTGGGCAAAAAAGTCTGTCATCTAAATTTCCTGCTCAGTATCTCTCCTATCGCCTTAAGGATGAGCATAACATGTCAATGACAGCTGAAGAAATT
AATTTCTTCAGCTGTCATTGACATGTTATGCTCATCCTTAAGGCGATAGGAGAGATACTGAGCAGGAAATTTAGATGACAGACTTTTTTGCCCAGGCAAA[AC/C]
CTCCGTAGGCATGCATTCATGATCCGCAACCTTCCCCACTTGAGCGTAAACACCATACCCAGCTTTGACCAAACTTCTGTAGTGCTTGATTTCAGAGCAA
| Populations | Population Size | Frequency of GT(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.80% | 0.20% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.30% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.60% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0727002572 | GT -> G | LOC_Os07g45250.1 | frameshift_variant ; p.Leu171fs; HIGH | N | Average:61.163; most accessible tissue: Callus, score: 88.336 | N | N | N | N |
| vg0727002572 | GT -> G | LOC_Os07g45194.1 | upstream_gene_variant ; 1547.0bp to feature; MODIFIER | N | Average:61.163; most accessible tissue: Callus, score: 88.336 | N | N | N | N |