| Variant ID: vg0825985206 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 25985206 |
| Reference Allele: G | Alternative Allele: GCTTGT |
| Primary Allele: G | Secondary Allele: GCTTGT |
Inferred Ancestral Allele: Not determined.
CGGCACGCCGATGCGCAGGGAGACGTACTCGCCATTGTCCTCCTCGCGGTAGCCGCGCGGGTAGCATCTGATGACCCACGACTGCTCCCCGTCGCCGACG[G/GCTTGT]
CGAAGCTGTTCGTCGTCGTCGTCGTCCCTGGGTACTCGAGCTTCAACTCGGCGAAGCTGGATGATATCATCATCGTATTTTTGGTGTATTATTAATTAAT
ATTAATTAATAATACACCAAAAATACGATGATGATATCATCCAGCTTCGCCGAGTTGAAGCTCGAGTACCCAGGGACGACGACGACGACGAACAGCTTCG[C/ACAAGC]
CGTCGGCGACGGGGAGCAGTCGTGGGTCATCAGATGCTACCCGCGCGGCTACCGCGAGGAGGACAATGGCGAGTACGTCTCCCTGCGCATCGGCGTGCCG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GCTTGT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 89.90% | 0.20% | 6.69% | 3.22% | NA |
| All Indica | 2759 | 85.10% | 0.20% | 9.86% | 4.78% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.13% | 0.33% | NA |
| Aus | 269 | 80.70% | 0.70% | 14.50% | 4.09% | NA |
| Indica I | 595 | 88.90% | 0.20% | 10.25% | 0.67% | NA |
| Indica II | 465 | 90.30% | 0.40% | 6.02% | 3.23% | NA |
| Indica III | 913 | 78.00% | 0.00% | 12.16% | 9.86% | NA |
| Indica Intermediate | 786 | 87.50% | 0.40% | 9.16% | 2.93% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.13% | 0.39% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 0.00% | 2.22% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0825985206 | G -> GCTTGT | LOC_Os08g41120.1 | frameshift_variant ; p.Ala25fs; HIGH | frameshift_variant | Average:80.884; most accessible tissue: Minghui63 young leaf, score: 88.629 | N | N | N | N |
| vg0825985206 | G -> DEL | LOC_Os08g41120.1 | N | frameshift_variant | Average:80.884; most accessible tissue: Minghui63 young leaf, score: 88.629 | N | N | N | N |