| Variant ID: vg0221508703 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 21508703 |
| Reference Allele: T | Alternative Allele: TTAG |
| Primary Allele: T | Secondary Allele: TTAG |
Inferred Ancestral Allele: Not determined.
GAGAGATCTTCTGAGCTCTCGCACTCTTTCGTGTGCGCCAAGCTTTTCCTGTTCAGCCCAATGGCCGAACAAGCAAAGGCGCACAACCTCTCTCCGAGCA[T/TTAG]
TAGCGGTGACGATGGGGAGCCAAACCCATGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCTAGGAGGGAGGAGGTGCTCGAGAGGGTC
GACCCTCTCGAGCACCTCCTCCCTCCTAGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCATGGGTTTGGCTCCCCATCGTCACCGCTA[A/CTAA]
TGCTCGGAGAGAGGTTGTGCGCCTTTGCTTGTTCGGCCATTGGGCTGAACAGGAAAAGCTTGGCGCACACGAAAGAGTGCGAGAGCTCAGAAGATCTCTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TTAG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.60% | 0.10% | 1.54% | 61.76% | NA |
| All Indica | 2759 | 4.40% | 0.20% | 1.92% | 93.51% | NA |
| All Japonica | 1512 | 96.80% | 0.00% | 0.20% | 3.04% | NA |
| Aus | 269 | 0.40% | 0.00% | 4.83% | 94.80% | NA |
| Indica I | 595 | 4.50% | 0.00% | 1.34% | 94.12% | NA |
| Indica II | 465 | 3.70% | 0.90% | 2.58% | 92.90% | NA |
| Indica III | 913 | 3.90% | 0.00% | 1.86% | 94.19% | NA |
| Indica Intermediate | 786 | 5.20% | 0.10% | 2.04% | 92.62% | NA |
| Temperate Japonica | 767 | 98.70% | 0.00% | 0.00% | 1.30% | NA |
| Tropical Japonica | 504 | 93.50% | 0.00% | 0.60% | 5.95% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 1.04% | 7.29% | NA |
| Intermediate | 90 | 62.20% | 0.00% | 3.33% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221508703 | T -> TTAG | LOC_Os02g35800.1 | disruptive_inframe_insertion ; p.Ser15dup; MODERATE | inframe_variant | Average:12.241; most accessible tissue: Callus, score: 31.066 | N | N | N | N |
| vg0221508703 | T -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:12.241; most accessible tissue: Callus, score: 31.066 | N | N | N | N |