| Variant ID: vg0123775932 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 23775932 |
| Reference Allele: C | Alternative Allele: CAA |
| Primary Allele: C | Secondary Allele: CAA |
Inferred Ancestral Allele: Not determined.
ATACTCACAAATTAATGCATACCCTAGAGTTTTTTTTTTTGAAATACACAAAAGACTTGCATATCATTGCATTAAGAGGAGTAAAGTAATACAAGACAGA[C/CAA]
AGAGAAGAACAGGGAGGAGAGAGGAGGGGAGGAGAAAAGGAGAAACGGAAAAAGACACACTAAATCACTGATCTCCCAAAACTATTGTGTGACCTAGACC
GGTCTAGGTCACACAATAGTTTTGGGAGATCAGTGATTTAGTGTGTCTTTTTCCGTTTCTCCTTTTCTCCTCCCCTCCTCTCTCCTCCCTGTTCTTCTCT[G/TTG]
TCTGTCTTGTATTACTTTACTCCTCTTAATGCAATGATATGCAAGTCTTTTGTGTATTTCAAAAAAAAAAACTCTAGGGTATGCATTAATTTGTGAGTAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 42.70% | 1.90% | 1.25% | 54.08% | NA |
| All Indica | 2759 | 11.20% | 0.10% | 1.99% | 86.70% | NA |
| All Japonica | 1512 | 86.80% | 5.50% | 0.26% | 7.41% | NA |
| Aus | 269 | 91.10% | 1.50% | 0.00% | 7.43% | NA |
| Indica I | 595 | 4.50% | 0.00% | 0.50% | 94.96% | NA |
| Indica II | 465 | 7.10% | 0.00% | 2.15% | 90.75% | NA |
| Indica III | 913 | 12.20% | 0.00% | 2.85% | 84.99% | NA |
| Indica Intermediate | 786 | 17.60% | 0.40% | 2.04% | 80.03% | NA |
| Temperate Japonica | 767 | 99.10% | 0.50% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 73.40% | 6.20% | 0.60% | 19.84% | NA |
| Japonica Intermediate | 241 | 75.90% | 19.90% | 0.41% | 3.73% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 64.40% | 1.10% | 0.00% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0123775932 | C -> DEL | N | N | silent_mutation | Average:13.979; most accessible tissue: Callus, score: 87.572 | N | N | N | N |
| vg0123775932 | C -> CAA | LOC_Os01g41930.1 | 5_prime_UTR_variant ; 568.0bp to feature; MODIFIER | silent_mutation | Average:13.979; most accessible tissue: Callus, score: 87.572 | N | N | N | N |
| vg0123775932 | C -> CAA | LOC_Os01g41920.1 | upstream_gene_variant ; 3250.0bp to feature; MODIFIER | silent_mutation | Average:13.979; most accessible tissue: Callus, score: 87.572 | N | N | N | N |
| vg0123775932 | C -> CAA | LOC_Os01g41910.1 | downstream_gene_variant ; 4418.0bp to feature; MODIFIER | silent_mutation | Average:13.979; most accessible tissue: Callus, score: 87.572 | N | N | N | N |