| Variant ID: vg1220960469 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 20960469 |
| Reference Allele: GA | Alternative Allele: G |
| Primary Allele: GA | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CCTCGCAAGCCTCACAAGGCATCTGAGGCGAGGAATTTGGCACCTCTAGAACTTGTTCATTCCGATTTGTGCGAAATGAACGGCGTGTTGACTAAAGGGG[GA/G]
AAGAAATATTTCATGACACTGATAGATGATTGCACTAGATTTTGCTATGTGTATCTATTGAAAACAAAGGATGAGGCATTGCATTTCTTTAAAATCTATA
TATAGATTTTAAAGAAATGCAATGCCTCATCCTTTGTTTTCAATAGATACACATAGCAAAATCTAGTGCAATCATCTATCAGTGTCATGAAATATTTCTT[TC/C]
CCCCTTTAGTCAACACGCCGTTCATTTCGCACAAATCGGAATGAACAAGTTCTAGAGGTGCCAAATTCCTCGCCTCAGATGCCTTGTGAGGCTTGCGAGG
| Populations | Population Size | Frequency of GA(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.90% | 0.10% | 0.51% | 40.46% | NA |
| All Indica | 2759 | 79.10% | 0.10% | 0.51% | 20.30% | NA |
| All Japonica | 1512 | 27.00% | 0.00% | 0.46% | 72.55% | NA |
| Aus | 269 | 52.00% | 0.00% | 0.74% | 47.21% | NA |
| Indica I | 595 | 63.00% | 0.00% | 0.84% | 36.13% | NA |
| Indica II | 465 | 78.90% | 0.20% | 0.22% | 20.65% | NA |
| Indica III | 913 | 88.60% | 0.20% | 0.22% | 10.95% | NA |
| Indica Intermediate | 786 | 80.20% | 0.10% | 0.76% | 18.96% | NA |
| Temperate Japonica | 767 | 10.40% | 0.00% | 0.26% | 89.31% | NA |
| Tropical Japonica | 504 | 48.40% | 0.00% | 0.79% | 50.79% | NA |
| Japonica Intermediate | 241 | 34.90% | 0.00% | 0.41% | 64.73% | NA |
| VI/Aromatic | 96 | 16.70% | 0.00% | 0.00% | 83.33% | NA |
| Intermediate | 90 | 44.40% | 1.10% | 1.11% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960469 | GA -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1220960469 | GA -> G | LOC_Os12g34580.1 | frameshift_variant ; p.Lys619fs; HIGH | frameshift_variant | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |