| Variant ID: vg0801635116 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 1635116 |
| Reference Allele: T | Alternative Allele: TC |
| Primary Allele: T | Secondary Allele: TC |
Inferred Ancestral Allele: Not determined.
GCGTCCCCCCTCGCCGGCGTGCCGGCGCCGGACCTGTCGAGGCACCTCGGCGAGCTGCTGGAGCGGGCGGACGGCGTGGGCGCGGACGTCACGTTCGACG[T/TC]
CAGGGGGCAACCCTTCGCCGCCCACCGGATCGTGCTCGCCATGCGCTCGCCGGTGTTCATGGCATCGCTGTACGGGTCGATGAGGGAGCACCGCGCGCCG
CGGCGCGCGGTGCTCCCTCATCGACCCGTACAGCGATGCCATGAACACCGGCGAGCGCATGGCGAGCACGATCCGGTGGGCGGCGAAGGGTTGCCCCCTG[A/GA]
CGTCGAACGTGACGTCCGCGCCCACGCCGTCCGCCCGCTCCAGCAGCTCGCCGAGGTGCCTCGACAGGTCCGGCGCCGGCACGCCGGCGAGGGGGGACGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.00% | 5.20% | 0.06% | 0.70% | NA |
| All Indica | 2759 | 97.70% | 1.00% | 0.07% | 1.20% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 19.70% | 79.90% | 0.37% | 0.00% | NA |
| Indica I | 595 | 97.60% | 0.00% | 0.00% | 2.35% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.50% | 0.90% | 0.00% | 0.66% | NA |
| Indica Intermediate | 786 | 95.70% | 2.40% | 0.25% | 1.65% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0801635116 | T -> DEL | LOC_Os08g03490.1 | N | frameshift_variant | Average:71.996; most accessible tissue: Zhenshan97 root, score: 83.259 | N | N | N | N |
| vg0801635116 | T -> TC | LOC_Os08g03490.1 | frameshift_variant ; p.Arg206fs; HIGH | frameshift_variant | Average:71.996; most accessible tissue: Zhenshan97 root, score: 83.259 | N | N | N | N |