| Variant ID: vg0318608662 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 18608662 |
| Reference Allele: GC | Alternative Allele: G |
| Primary Allele: GC | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TGGAGTCCGCGACGAGGCGGACGTAGTCCCAGCTGAGGACGATCTTGTGGAAGCGGTCCATGGTGGAGGCGGCGACGCCCGACGAGGAGGAGGAGGCGCC[GC/G]
CTCCGCCTCCGCCGCCGCCGGATTTGTCCACCGCCATTGGGGCGGCGGCGCGGCGGCGCGGCGGCGAGAGAAGGGGGTTCTGGGGTTTAGTGAGCCGCCG
CGGCGGCTCACTAAACCCCAGAACCCCCTTCTCTCGCCGCCGCGCCGCCGCGCCGCCGCCCCAATGGCGGTGGACAAATCCGGCGGCGGCGGAGGCGGAG[GC/C]
GGCGCCTCCTCCTCCTCGTCGGGCGTCGCCGCCTCCACCATGGACCGCTTCCACAAGATCGTCCTCAGCTGGGACTACGTCCGCCTCGTCGCGGACTCCA
| Populations | Population Size | Frequency of GC(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.30% | 0.20% | 0.40% | 0.13% | NA |
| All Indica | 2759 | 99.50% | 0.00% | 0.33% | 0.22% | NA |
| All Japonica | 1512 | 99.10% | 0.30% | 0.60% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 98.10% | 0.00% | 1.08% | 0.86% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.00% | 0.38% | 0.25% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.40% | 0.80% | 1.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 5.20% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0318608662 | GC -> DEL | LOC_Os03g32526.1 | N | frameshift_variant | Average:32.259; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg0318608662 | GC -> G | LOC_Os03g32526.1 | frameshift_variant ; p.Gly13fs; HIGH | frameshift_variant | Average:32.259; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |