| Variant ID: vg0205101625 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 5101625 |
| Reference Allele: C | Alternative Allele: CA,CACA |
| Primary Allele: C | Secondary Allele: CA |
Inferred Ancestral Allele: Not determined.
GTATAGCTCCTTGTTTCGTCTGACGTGACGCTTTGACCGTGGTCTGCTTTGCTGAGTCAACGTAGCTTACTGTGGGGCTGTGTTTGAAATCATCTTCTCC[C/CA,CACA]
CCCCCCCCCCTCTTCCTGTTTCTCTATCTTCCCCCACAATGGAGCGATGGTGGCGCCCGGAGCAGTGCATCAGCGAGGAGAGCGGCGTCGTGTTGGGTTT
AAACCCAACACGACGCCGCTCTCCTCGCTGATGCACTGCTCCGGGCGCCACCATCGCTCCATTGTGGGGGAAGATAGAGAAACAGGAAGAGGGGGGGGGG[G/TG,TGTG]
GGAGAAGATGATTTCAAACACAGCCCCACAGTAAGCTACGTTGACTCAGCAAAGCAGACCACGGTCAAAGCGTCACGTCAGACGAAACAAGGAGCTATAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.00% | 5.80% | 36.69% | 19.51% | CACA: 0.02% |
| All Indica | 2759 | 35.00% | 7.30% | 34.94% | 22.73% | CACA: 0.04% |
| All Japonica | 1512 | 47.60% | 1.60% | 40.08% | 10.71% | NA |
| Aus | 269 | 21.60% | 14.10% | 39.41% | 24.91% | NA |
| Indica I | 595 | 47.60% | 0.50% | 37.65% | 14.29% | NA |
| Indica II | 465 | 25.40% | 6.50% | 27.53% | 40.65% | NA |
| Indica III | 913 | 35.20% | 10.70% | 35.60% | 18.40% | CACA: 0.11% |
| Indica Intermediate | 786 | 31.00% | 8.90% | 36.51% | 23.54% | NA |
| Temperate Japonica | 767 | 33.20% | 0.50% | 54.76% | 11.47% | NA |
| Tropical Japonica | 504 | 66.70% | 2.20% | 21.23% | 9.92% | NA |
| Japonica Intermediate | 241 | 53.50% | 3.70% | 32.78% | 9.96% | NA |
| VI/Aromatic | 96 | 19.80% | 5.20% | 28.12% | 46.88% | NA |
| Intermediate | 90 | 37.80% | 4.40% | 34.44% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0205101625 | C -> CA | LOC_Os02g09870.1 | upstream_gene_variant ; 2795.0bp to feature; MODIFIER | silent_mutation | Average:77.347; most accessible tissue: Minghui63 panicle, score: 86.85 | N | N | N | N |
| vg0205101625 | C -> CA | LOC_Os02g09870-LOC_Os02g09880 | intergenic_region ; MODIFIER | silent_mutation | Average:77.347; most accessible tissue: Minghui63 panicle, score: 86.85 | N | N | N | N |
| vg0205101625 | C -> CACA | LOC_Os02g09870.1 | upstream_gene_variant ; 2795.0bp to feature; MODIFIER | silent_mutation | Average:77.347; most accessible tissue: Minghui63 panicle, score: 86.85 | N | N | N | N |
| vg0205101625 | C -> CACA | LOC_Os02g09870-LOC_Os02g09880 | intergenic_region ; MODIFIER | silent_mutation | Average:77.347; most accessible tissue: Minghui63 panicle, score: 86.85 | N | N | N | N |
| vg0205101625 | C -> DEL | N | N | silent_mutation | Average:77.347; most accessible tissue: Minghui63 panicle, score: 86.85 | N | N | N | N |