| Variant ID: vg0524150679 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 24150679 |
| Reference Allele: CA | Alternative Allele: C,CAA |
| Primary Allele: C | Secondary Allele: CA |
Inferred Ancestral Allele: Not determined.
CTTGCAACTCTCTACAAAGAGAAGCACTAGCAAATTAAACTACATTGACATTAGTCTGCTAAATGTGCCTTTTCATTTCTTTCTTGACAACAATAACAAA[CA/C,CAA]
AAAAAAAACACAACTTTAATTTGCATGATTGATTACAAGAGCTTACATAAATTGTAGCTGGTCCAGTCGCGCAAGATCGGCCGACAGATGGCCGGACAGG
CCTGTCCGGCCATCTGTCGGCCGATCTTGCGCGACTGGACCAGCTACAATTTATGTAAGCTCTTGTAATCAATCATGCAAATTAAAGTTGTGTTTTTTTT[TG/G,TTG]
TTTGTTATTGTTGTCAAGAAAGAAATGAAAAGGCACATTTAGCAGACTAATGTCAATGTAGTTTAATTTGCTAGTGCTTCTCTTTGTAGAGAGTTGCAAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.70% | 48.40% | 0.61% | 0.28% | CAA: 1.06% |
| All Indica | 2759 | 72.30% | 24.50% | 1.01% | 0.47% | CAA: 1.74% |
| All Japonica | 1512 | 0.60% | 99.20% | 0.07% | 0.00% | CAA: 0.13% |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 80.80% | 17.60% | 1.34% | 0.00% | CAA: 0.17% |
| Indica II | 465 | 67.50% | 31.00% | 0.43% | 1.08% | NA |
| Indica III | 913 | 68.50% | 26.20% | 0.33% | 0.55% | CAA: 4.49% |
| Indica Intermediate | 786 | 73.00% | 23.90% | 1.91% | 0.38% | CAA: 0.76% |
| Temperate Japonica | 767 | 0.10% | 99.60% | 0.13% | 0.00% | CAA: 0.13% |
| Tropical Japonica | 504 | 1.60% | 98.20% | 0.00% | 0.00% | CAA: 0.20% |
| Japonica Intermediate | 241 | 0.00% | 100.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 36.50% | 63.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 47.80% | 52.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0524150679 | CA -> DEL | N | N | silent_mutation | Average:69.975; most accessible tissue: Callus, score: 97.584 | N | N | N | N |
| vg0524150679 | CA -> CAA | LOC_Os05g41240.1 | downstream_gene_variant ; 3052.0bp to feature; MODIFIER | silent_mutation | Average:69.975; most accessible tissue: Callus, score: 97.584 | N | N | N | N |
| vg0524150679 | CA -> CAA | LOC_Os05g41240.3 | downstream_gene_variant ; 3052.0bp to feature; MODIFIER | silent_mutation | Average:69.975; most accessible tissue: Callus, score: 97.584 | N | N | N | N |
| vg0524150679 | CA -> CAA | LOC_Os05g41240.2 | downstream_gene_variant ; 3052.0bp to feature; MODIFIER | silent_mutation | Average:69.975; most accessible tissue: Callus, score: 97.584 | N | N | N | N |
| vg0524150679 | CA -> CAA | LOC_Os05g41230.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.975; most accessible tissue: Callus, score: 97.584 | N | N | N | N |
| vg0524150679 | CA -> C | LOC_Os05g41240.1 | downstream_gene_variant ; 3053.0bp to feature; MODIFIER | silent_mutation | Average:69.975; most accessible tissue: Callus, score: 97.584 | N | N | N | N |
| vg0524150679 | CA -> C | LOC_Os05g41240.3 | downstream_gene_variant ; 3053.0bp to feature; MODIFIER | silent_mutation | Average:69.975; most accessible tissue: Callus, score: 97.584 | N | N | N | N |
| vg0524150679 | CA -> C | LOC_Os05g41240.2 | downstream_gene_variant ; 3053.0bp to feature; MODIFIER | silent_mutation | Average:69.975; most accessible tissue: Callus, score: 97.584 | N | N | N | N |
| vg0524150679 | CA -> C | LOC_Os05g41230.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.975; most accessible tissue: Callus, score: 97.584 | N | N | N | N |