| Variant ID: vg0409515543 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 9515543 |
| Reference Allele: AAT | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: AAT |
Inferred Ancestral Allele: Not determined.
CTATCAAACCGTCTTGCAATTCTATCCTTCTAGAGCCGATTCTAACTTCCCATGGCAAAACAGCTTCATGTCCATAAACAAGCTTATAAGGAGGAACTTG[AAT/A]
ATTGATCCATGACAAGCCATCCGATAAGACCACAATGCTTCGGCCAACCGGGTATGCCATTGCTGAGGATAATCAGAAATCTTCCGCTTAATTAATTTGA
TCAAATTAATTAAGCGGAAGATTTCTGATTATCCTCAGCAATGGCATACCCGGTTGGCCGAAGCATTGTGGTCTTATCGGATGGCTTGTCATGGATCAAT[ATT/T]
CAAGTTCCTCCTTATAAGCTTGTTTATGGACATGAAGCTGTTTTGCCATGGGAAGTTAGAATCGGCTCTAGAAGGATAGAATTGCAAGACGGTTTGATAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AAT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.40% | 23.70% | 0.53% | 10.28% | NA |
| All Indica | 2759 | 98.40% | 1.30% | 0.18% | 0.14% | NA |
| All Japonica | 1512 | 2.60% | 69.20% | 0.00% | 28.17% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.30% | 1.30% | 0.34% | 0.00% | NA |
| Indica II | 465 | 97.20% | 2.20% | 0.00% | 0.65% | NA |
| Indica III | 913 | 99.50% | 0.40% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 98.00% | 1.70% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 0.90% | 97.50% | 0.00% | 1.56% | NA |
| Tropical Japonica | 504 | 4.20% | 23.20% | 0.00% | 72.62% | NA |
| Japonica Intermediate | 241 | 5.00% | 75.10% | 0.00% | 19.92% | NA |
| VI/Aromatic | 96 | 21.90% | 10.40% | 14.58% | 53.12% | NA |
| Intermediate | 90 | 55.60% | 32.20% | 6.67% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515543 | AAT -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:24.01; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 | N | N | N | N |
| vg0409515543 | AAT -> A | LOC_Os04g17380.1 | frameshift_variant ; p.Ile21fs; HIGH | frameshift_variant | Average:24.01; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 | N | N | N | N |