| Variant ID: vg0918112495 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr09 | Position: 18112495 |
| Reference Allele: AT | Alternative Allele: A,ATT |
| Primary Allele: AT | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCACCTTCTCTAATAGAACCCACCCTTGAGGAGTTGATTTGCATGATGTTACTATGTAAATTGCACCATGAACTGTTTGGCTGCCAATAAAGGTTAACAC[AT/A,ATT]
TTTTTTTTTCGAATAGAGAGATCAAAGAAGGCTCAACAAATCTAGTGCTTTTAAAATAGATTGGGAAAACAGAGTTCTGTAAAAAAAAACGGAGTTGCAA
TTGCAACTCCGTTTTTTTTTACAGAACTCTGTTTTCCCAATCTATTTTAAAAGCACTAGATTTGTTGAGCCTTCTTTGATCTCTCTATTCGAAAAAAAAA[AT/T,AAT]
GTGTTAACCTTTATTGGCAGCCAAACAGTTCATGGTGCAATTTACATAGTAACATCATGCAAATCAACTCCTCAAGGGTGGGTTCTATTAGAGAAGGTGA
| Populations | Population Size | Frequency of AT(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.00% | 0.80% | 0.08% | 0.00% | ATT: 0.08% |
| All Indica | 2759 | 98.60% | 1.30% | 0.07% | 0.00% | ATT: 0.04% |
| All Japonica | 1512 | 99.90% | 0.10% | 0.07% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.40% | 0.00% | 0.00% | ATT: 0.37% |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.10% | 3.60% | 0.22% | 0.00% | ATT: 0.11% |
| Indica Intermediate | 786 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 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 | 95.60% | 1.10% | 1.11% | 0.00% | ATT: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0918112495 | AT -> ATT | LOC_Os09g29790.1 | upstream_gene_variant ; 3184.0bp to feature; MODIFIER | silent_mutation | Average:37.09; most accessible tissue: Callus, score: 80.523 | N | N | N | N |
| vg0918112495 | AT -> ATT | LOC_Os09g29810.1 | upstream_gene_variant ; 2628.0bp to feature; MODIFIER | silent_mutation | Average:37.09; most accessible tissue: Callus, score: 80.523 | N | N | N | N |
| vg0918112495 | AT -> ATT | LOC_Os09g29800.1 | intron_variant ; MODIFIER | silent_mutation | Average:37.09; most accessible tissue: Callus, score: 80.523 | N | N | N | N |
| vg0918112495 | AT -> A | LOC_Os09g29790.1 | upstream_gene_variant ; 3183.0bp to feature; MODIFIER | silent_mutation | Average:37.09; most accessible tissue: Callus, score: 80.523 | N | N | N | N |
| vg0918112495 | AT -> A | LOC_Os09g29810.1 | upstream_gene_variant ; 2629.0bp to feature; MODIFIER | silent_mutation | Average:37.09; most accessible tissue: Callus, score: 80.523 | N | N | N | N |
| vg0918112495 | AT -> A | LOC_Os09g29800.1 | intron_variant ; MODIFIER | silent_mutation | Average:37.09; most accessible tissue: Callus, score: 80.523 | N | N | N | N |