| Variant ID: vg0629027041 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 29027041 |
| Reference Allele: AT | Alternative Allele: A |
| Primary Allele: AT | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACTGCACGTCAAGTCAAGTCAAACACAAATTAATCGAACAAATCACTTTTACATCGTTGTATATTACAACTTATTCGGATCGTTGACAAAAACAACTTAA[AT/A]
TTTTGAACACACAATAATGTACTACCGATTGTTTTTTCCCCAAATCCAAAAGGAAAGATTGCCATCTATCGCCCAATTGCCCTCCAAGAACATGCAACCT
AGGTTGCATGTTCTTGGAGGGCAATTGGGCGATAGATGGCAATCTTTCCTTTTGGATTTGGGGAAAAAACAATCGGTAGTACATTATTGTGTGTTCAAAA[AT/T]
TTAAGTTGTTTTTGTCAACGATCCGAATAAGTTGTAATATACAACGATGTAAAAGTGATTTGTTCGATTAATTTGTGTTTGACTTGACTTGACGTGCAGT
| 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 | 89.90% | 10.10% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 83.10% | 16.90% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 91.60% | 8.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 74.50% | 25.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 78.40% | 21.40% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 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 | 91.10% | 8.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0629027041 | AT -> A | LOC_Os06g48010.1 | 3_prime_UTR_variant ; 181.0bp to feature; MODIFIER | silent_mutation | Average:65.181; most accessible tissue: Callus, score: 80.658 | N | N | N | N |
| vg0629027041 | AT -> A | LOC_Os06g48000.1 | downstream_gene_variant ; 3550.0bp to feature; MODIFIER | silent_mutation | Average:65.181; most accessible tissue: Callus, score: 80.658 | N | N | N | N |