| Variant ID: vg0138753539 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 38753539 |
| Reference Allele: CT | Alternative Allele: CTT,C |
| Primary Allele: CT | Secondary Allele: CTT |
Inferred Ancestral Allele: Not determined.
AGTGCTTCTATTTCATAGTTTTCGTACTGAATGGAAAATATTTAGTTACATACTGATATATGAATCTGCTCCCCCCGTTTCCTATCATAAGTCATTTTGA[CT/CTT,C]
TTTTTTTTCTTAATTAAACTTCTTTAGGTTAGATCAAGTTTATAGAAAAAATATAGCAACATTTCTAAAAACAAACATGTTATCAAAATGTATTCAATGT
ACATTGAATACATTTTGATAACATGTTTGTTTTTAGAAATGTTGCTATATTTTTTCTATAAACTTGATCTAACCTAAAGAAGTTTAATTAAGAAAAAAAA[AG/AAG,G]
TCAAAATGACTTATGATAGGAAACGGGGGGAGCAGATTCATATATCAGTATGTAACTAAATATTTTCCATTCAGTACGAAAACTATGAAATAGAAGCACT
| Populations | Population Size | Frequency of CT(primary allele) | Frequency of CTT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.20% | 2.50% | 0.28% | 0.00% | C: 0.11% |
| All Indica | 2759 | 98.90% | 0.90% | 0.07% | 0.00% | C: 0.14% |
| All Japonica | 1512 | 98.90% | 0.40% | 0.66% | 0.00% | C: 0.07% |
| Aus | 269 | 74.00% | 26.00% | 0.00% | 0.00% | NA |
| 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 | 97.70% | 2.20% | 0.00% | 0.00% | C: 0.11% |
| Indica Intermediate | 786 | 98.70% | 0.60% | 0.25% | 0.00% | C: 0.38% |
| Temperate Japonica | 767 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 1.70% | 0.83% | 0.00% | C: 0.41% |
| VI/Aromatic | 96 | 87.50% | 12.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 3.30% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0138753539 | CT -> CTT | LOC_Os01g66710.1 | downstream_gene_variant ; 2773.0bp to feature; MODIFIER | silent_mutation | Average:38.32; most accessible tissue: Callus, score: 72.221 | N | N | N | N |
| vg0138753539 | CT -> CTT | LOC_Os01g66730.1 | downstream_gene_variant ; 1517.0bp to feature; MODIFIER | silent_mutation | Average:38.32; most accessible tissue: Callus, score: 72.221 | N | N | N | N |
| vg0138753539 | CT -> CTT | LOC_Os01g66730.2 | downstream_gene_variant ; 1545.0bp to feature; MODIFIER | silent_mutation | Average:38.32; most accessible tissue: Callus, score: 72.221 | N | N | N | N |
| vg0138753539 | CT -> CTT | LOC_Os01g66720.1 | intron_variant ; MODIFIER | silent_mutation | Average:38.32; most accessible tissue: Callus, score: 72.221 | N | N | N | N |
| vg0138753539 | CT -> C | LOC_Os01g66710.1 | downstream_gene_variant ; 2772.0bp to feature; MODIFIER | silent_mutation | Average:38.32; most accessible tissue: Callus, score: 72.221 | N | N | N | N |
| vg0138753539 | CT -> C | LOC_Os01g66730.1 | downstream_gene_variant ; 1518.0bp to feature; MODIFIER | silent_mutation | Average:38.32; most accessible tissue: Callus, score: 72.221 | N | N | N | N |
| vg0138753539 | CT -> C | LOC_Os01g66730.2 | downstream_gene_variant ; 1546.0bp to feature; MODIFIER | silent_mutation | Average:38.32; most accessible tissue: Callus, score: 72.221 | N | N | N | N |
| vg0138753539 | CT -> C | LOC_Os01g66720.1 | intron_variant ; MODIFIER | silent_mutation | Average:38.32; most accessible tissue: Callus, score: 72.221 | N | N | N | N |