| Variant ID: vg0825998056 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 25998056 |
| Reference Allele: GCCGTGGAGCCGAGGAGCTCCA | Alternative Allele: G |
| Primary Allele: GCCGTGGAGCCGAGGAGCTC CA | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTCGATGATCTGCAGAACGTCCGTGTACACGAAGTGCAGCAGAGCTCTGAACGTCGTCGGCTCGATGTCATGCAGCGTGACGCACGGCATGGTGGCCTCC[GCCGTGGAGCCGAGGAGCTCCA/G]
CCCTGAACACCGGCGAGCGCGCGGCGAGCACGGCCCGGTGCGCGTGGAACGTCTCACCGCCGACGGAGAAGGACACGTCCGAGCCGTCGGCGCTGCCCAC
GTGGGCAGCGCCGACGGCTCGGACGTGTCCTTCTCCGTCGGCGGTGAGACGTTCCACGCGCACCGGGCCGTGCTCGCCGCGCGCTCGCCGGTGTTCAGGG[TGGAGCTCCTCGGCTCCACGGC/C]
GGAGGCCACCATGCCGTGCGTCACGCTGCATGACATCGAGCCGACGACGTTCAGAGCTCTGCTGCACTTCGTGTACACGGACGTTCTGCAGATCATCGAG
| Populations | Population Size | Frequency of GCCGTGGAGCCGAGGAGCTC CA(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.30% | 5.70% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 32.70% | 67.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 90.60% | 9.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0825998056 | GCCGTGGAGCCGAGGAGCTCCA -> G | LOC_Os08g41150.1 | disruptive_inframe_deletion ; p.Val208_Thr214del; MODERATE | inframe_variant | Average:74.959; most accessible tissue: Zhenshan97 panicle, score: 85.665 | N | N | N | N |