| Variant ID: vg0910530353 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr09 | Position: 10530353 |
| Reference Allele: C | Alternative Allele: CG |
| Primary Allele: C | Secondary Allele: CG |
Inferred Ancestral Allele: Not determined.
CACCTGCCTCACTCAGGGGTGAACCATCTATGCAGGGATACTGCCTCCGCTCGGCTATCTAATCCGCTAGGTCTATACCTATTCGAGAAGTACGGTTGTA[C/CG]
GGGGGTCGTTTCATGCTTAACTTCATGGCCCAGTCCTTAATTGACCGGGGACGGTACTAGCCTTTTCCAGATACCACCCAAATCCTCCGTCCGCCCCAGT
ACTGGGGCGGACGGAGGATTTGGGTGGTATCTGGAAAAGGCTAGTACCGTCCCCGGTCAATTAAGGACTGGGCCATGAAGTTAAGCATGAAACGACCCCC[G/CG]
TACAACCGTACTTCTCGAATAGGTATAGACCTAGCGGATTAGATAGCCGAGCGGAGGCAGTATCCCTGCATAGATGGTTCACCCCTGAGTGAGGCAGGTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 12.00% | 0.10% | 25.20% | 62.67% | NA |
| All Indica | 2759 | 4.80% | 0.20% | 24.43% | 70.57% | NA |
| All Japonica | 1512 | 25.60% | 0.00% | 23.08% | 51.32% | NA |
| Aus | 269 | 11.90% | 0.70% | 27.14% | 60.22% | NA |
| Indica I | 595 | 6.60% | 0.30% | 26.89% | 66.22% | NA |
| Indica II | 465 | 1.50% | 0.00% | 24.73% | 73.76% | NA |
| Indica III | 913 | 5.90% | 0.20% | 22.45% | 71.41% | NA |
| Indica Intermediate | 786 | 4.20% | 0.10% | 24.68% | 70.99% | NA |
| Temperate Japonica | 767 | 46.30% | 0.00% | 7.95% | 45.76% | NA |
| Tropical Japonica | 504 | 2.00% | 0.00% | 47.22% | 50.79% | NA |
| Japonica Intermediate | 241 | 9.10% | 0.00% | 20.75% | 70.12% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 62.50% | 34.38% | NA |
| Intermediate | 90 | 12.20% | 0.00% | 38.89% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910530353 | C -> DEL | LOC_Os09g17160.1 | N | frameshift_variant | Average:9.382; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg0910530353 | C -> CG | LOC_Os09g17160.1 | N | frameshift_variant | Average:9.382; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |