| Variant ID: vg0322195585 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 22195585 |
| Reference Allele: CGG | Alternative Allele: C |
| Primary Allele: CGG | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TTCCCGGAGGCGGTCCGCGGCTTCTCGCCGGTCAGCTTCCCGCCTCCGGGCCTCCGCTGTCGCCGTCTCCTCGGCCTCAGACCGGCCGGACTTGGAATGG[CGG/C]
GGGGGGGGCGCGACGGGATCTCGCTGAGGCAGAAGAAAAACCAGAAGACAAAAAGAAACGGGTGAGTGAAAACTCGCCTTGGGAGATGGGAGAATAAATA
TATTTATTCTCCCATCTCCCAAGGCGAGTTTTCACTCACCCGTTTCTTTTTGTCTTCTGGTTTTTCTTCTGCCTCAGCGAGATCCCGTCGCGCCCCCCCC[CCG/G]
CCATTCCAAGTCCGGCCGGTCTGAGGCCGAGGAGACGGCGACAGCGGAGGCCCGGAGGCGGGAAGCTGACCGGCGAGAAGCCGCGGACCGCCTCCGGGAA
| Populations | Population Size | Frequency of CGG(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 2.20% | 0.50% | 23.47% | 73.83% | NA |
| All Indica | 2759 | 2.40% | 0.00% | 22.25% | 75.39% | NA |
| All Japonica | 1512 | 1.50% | 1.40% | 27.05% | 70.04% | NA |
| Aus | 269 | 5.20% | 0.00% | 26.77% | 68.03% | NA |
| Indica I | 595 | 0.50% | 0.00% | 10.08% | 89.41% | NA |
| Indica II | 465 | 1.10% | 0.00% | 7.74% | 91.18% | NA |
| Indica III | 913 | 5.50% | 0.00% | 41.95% | 52.57% | NA |
| Indica Intermediate | 786 | 0.90% | 0.00% | 17.18% | 81.93% | NA |
| Temperate Japonica | 767 | 1.00% | 0.50% | 18.64% | 79.79% | NA |
| Tropical Japonica | 504 | 1.60% | 3.00% | 40.28% | 55.16% | NA |
| Japonica Intermediate | 241 | 2.90% | 0.80% | 26.14% | 70.12% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 4.17% | 93.75% | NA |
| Intermediate | 90 | 2.20% | 1.10% | 11.11% | 85.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322195585 | CGG -> C | LOC_Os03g39930.1 | 5_prime_UTR_variant ; 465.0bp to feature; MODIFIER | silent_mutation | Average:20.77; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0322195585 | CGG -> C | LOC_Os03g39920.1 | downstream_gene_variant ; 2416.0bp to feature; MODIFIER | silent_mutation | Average:20.77; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0322195585 | CGG -> C | LOC_Os03g39940.1 | downstream_gene_variant ; 2309.0bp to feature; MODIFIER | silent_mutation | Average:20.77; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0322195585 | CGG -> DEL | N | N | silent_mutation | Average:20.77; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |