| Variant ID: vg0114526835 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 14526835 |
| Reference Allele: GT | Alternative Allele: G |
| Primary Allele: GT | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGCATCTCTACCAAATCGACAATATAGCATCTCCAAGGCTTCGAGATAGTACTAGATAATAAATCTGCTTTCCAGGTCGTGTTGATAACAGATCTGCTTG[GT/G]
TAACTTCCTAAGTATCTGTCTATGTTGCTATGAACAGAACACAATCATGTGCCTTGTGTTCTGGCGAAAAAGGTTACTATCATGTGCGGATTGCATATTT
AAATATGCAATCCGCACATGATAGTAACCTTTTTCGCCAGAACACAAGGCACATGATTGTGTTCTGTTCATAGCAACATAGACAGATACTTAGGAAGTTA[AC/C]
CAAGCAGATCTGTTATCAACACGACCTGGAAAGCAGATTTATTATCTAGTACTATCTCGAAGCCTTGGAGATGCTATATTGTCGATTTGGTAGAGATGCC
| Populations | Population Size | Frequency of GT(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.00% | 0.70% | 0.17% | 4.04% | NA |
| All Indica | 2759 | 91.70% | 1.20% | 0.22% | 6.85% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
| Aus | 269 | 98.50% | 0.70% | 0.37% | 0.37% | NA |
| Indica I | 595 | 95.10% | 0.00% | 0.00% | 4.87% | NA |
| Indica II | 465 | 94.20% | 3.00% | 0.00% | 2.80% | NA |
| Indica III | 913 | 91.50% | 0.10% | 0.22% | 8.21% | NA |
| Indica Intermediate | 786 | 88.00% | 2.30% | 0.51% | 9.16% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114526835 | GT -> G | LOC_Os01g25630.1 | intron_variant ; MODIFIER | silent_mutation | Average:49.312; most accessible tissue: Zhenshan97 flower, score: 77.755 | N | N | N | N |
| vg0114526835 | GT -> DEL | N | N | silent_mutation | Average:49.312; most accessible tissue: Zhenshan97 flower, score: 77.755 | N | N | N | N |