| Variant ID: vg1201715494 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 1715494 |
| Reference Allele: CCGA | Alternative Allele: C |
| Primary Allele: CCGA | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CAAGAGTTCCGTCGAGGGGTGTACCAGGGAGAGGTGTACTGGGCTGGCCGAGTGATCAGGCCTCGTCCTTCGCCCATGCTAGGACGACGTCGCCGCGCCG[CCGA/C]
CGGGGATGCCCCGATGCAAGATGTCGCGAGATGTCCTCCTGGGCCTCGCGCTGACGAAGGCGTGCGACGCGAGGCAGGAGGAGTGCGCCGTGTGCCTCAG
CTGAGGCACACGGCGCACTCCTCCTGCCTCGCGTCGCACGCCTTCGTCAGCGCGAGGCCCAGGAGGACATCTCGCGACATCTTGCATCGGGGCATCCCCG[TCGG/G]
CGGCGCGGCGACGTCGTCCTAGCATGGGCGAAGGACGAGGCCTGATCACTCGGCCAGCCCAGTACACCTCTCCCTGGTACACCCCTCGACGGAACTCTTG
| Populations | Population Size | Frequency of CCGA(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 44.60% | 1.40% | 1.88% | 52.09% | NA |
| All Indica | 2759 | 9.30% | 2.40% | 3.01% | 85.25% | NA |
| All Japonica | 1512 | 97.30% | 0.10% | 0.07% | 2.58% | NA |
| Aus | 269 | 83.30% | 0.00% | 1.49% | 15.24% | NA |
| Indica I | 595 | 2.50% | 0.80% | 2.69% | 93.95% | NA |
| Indica II | 465 | 6.00% | 2.20% | 2.37% | 89.46% | NA |
| Indica III | 913 | 11.70% | 3.70% | 3.07% | 81.49% | NA |
| Indica Intermediate | 786 | 13.60% | 2.30% | 3.56% | 80.53% | NA |
| Temperate Japonica | 767 | 95.70% | 0.10% | 0.00% | 4.17% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 68.90% | 0.00% | 1.11% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1201715494 | CCGA -> C | LOC_Os12g04090.1 | inframe_deletion ; p.Thr108del; MODERATE | inframe_variant | Average:71.118; most accessible tissue: Callus, score: 91.31 | N | N | N | N |
| vg1201715494 | CCGA -> DEL | LOC_Os12g04090.1 | N | frameshift_variant | Average:71.118; most accessible tissue: Callus, score: 91.31 | N | N | N | N |