| Variant ID: vg0409515519 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 9515519 |
| Reference Allele: AACAAGCTTATAAGGAGGAACTTGAATATTGATCCATG | Alternative Allele: A |
| Primary Allele: AACAAGCTTATAAGGAGGAA CTTGAATATTGATCCATG | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCATAAGGTTATAATATTCATCGGCTATCAAACCGTCTTGCAATTCTATCCTTCTAGAGCCGATTCTAACTTCCCATGGCAAAACAGCTTCATGTCCATA[AACAAGCTTATAAGGAGGAACTTGAATATTGATCCATG/A]
ACAAGCCATCCGATAAGACCACAATGCTTCGGCCAACCGGGTATGCCATTGCTGAGGATAATCAGAAATCTTCCGCTTAATTAATTTGATCAAGCTCTTG
CAAGAGCTTGATCAAATTAATTAAGCGGAAGATTTCTGATTATCCTCAGCAATGGCATACCCGGTTGGCCGAAGCATTGTGGTCTTATCGGATGGCTTGT[CATGGATCAATATTCAAGTTCCTCCTTATAAGCTTGTT/T]
TATGGACATGAAGCTGTTTTGCCATGGGAAGTTAGAATCGGCTCTAGAAGGATAGAATTGCAAGACGGTTTGATAGCCGATGAATATTATAACCTTATGG
| Populations | Population Size | Frequency of AACAAGCTTATAAGGAGGAA CTTGAATATTGATCCATG(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.20% | 0.00% | 0.83% | 8.93% | NA |
| All Indica | 2759 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
| All Japonica | 1512 | 73.10% | 0.10% | 0.73% | 26.06% | 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 | 98.80% | 0.00% | 1.20% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 31.20% | 0.00% | 1.79% | 67.06% | NA |
| Japonica Intermediate | 241 | 80.10% | 0.40% | 0.83% | 18.67% | NA |
| VI/Aromatic | 96 | 58.30% | 1.00% | 12.50% | 28.12% | NA |
| Intermediate | 90 | 94.40% | 0.00% | 4.44% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515519 | AACAAGCTTATAAGGAGGAACTTGAATATTGATCCATG -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:23.54; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 | N | N | N | N |
| vg0409515519 | AACAAGCTTATAAGGAGGAACTTGAATATTGATCCATG -> A | LOC_Os04g17380.1 | frameshift_variant ; p.Ser17fs; HIGH | frameshift_variant | Average:23.54; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 | N | N | N | N |