| Variant ID: vg0315011678 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 15011678 |
| Reference Allele: CGGAGGTAGT | Alternative Allele: TGGAGGTAGT,C |
| Primary Allele: CGGAGGTAGT | Secondary Allele: TGGAGGTAGT |
Inferred Ancestral Allele: Not determined.
ACAACTCATAACAAAATAAATTACAATTACGTAAATTTTTTGAATAAGACAAATGGTCAAACATGTGAGAAAAAGTCAACGGCGTCATCTATTAAAAAAA[CGGAGGTAGT/TGGAGGTAGT,C]
ATGTTATTCCCTTTTCTGCATCCATGATAGATATTGCCTCTGGTTTTAAATGGACAAATCGGACGTCTGGCATTTCTCAGAACATCGGACGGTGTATTTG
CAAATACACCGTCCGATGTTCTGAGAAATGCCAGACGTCCGATTTGTCCATTTAAAACCAGAGGCAATATCTATCATGGATGCAGAAAAGGGAATAACAT[ACTACCTCCG/ACTACCTCCA,G]
TTTTTTTAATAGATGACGCCGTTGACTTTTTCTCACATGTTTGACCATTTGTCTTATTCAAAAAATTTACGTAATTGTAATTTATTTTGTTATGAGTTGT
| Populations | Population Size | Frequency of CGGAGGTAGT(primary allele) | Frequency of TGGAGGTAGT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.20% | 1.80% | 0.49% | 0.00% | C: 0.51% |
| All Indica | 2759 | 95.40% | 3.00% | 0.80% | 0.00% | C: 0.83% |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.20% | 0.00% | 1.18% | 0.00% | C: 0.67% |
| Indica II | 465 | 90.10% | 6.50% | 1.94% | 0.00% | C: 1.51% |
| Indica III | 913 | 94.70% | 5.10% | 0.00% | 0.00% | C: 0.11% |
| Indica Intermediate | 786 | 97.20% | 0.60% | 0.76% | 0.00% | C: 1.40% |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 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 | 96.70% | 1.10% | 1.11% | 0.00% | C: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0315011678 | CGGAGGTAGT -> C | LOC_Os03g26240.1 | upstream_gene_variant ; 2226.0bp to feature; MODIFIER | silent_mutation | Average:41.23; most accessible tissue: Callus, score: 67.433 | N | N | N | N |
| vg0315011678 | CGGAGGTAGT -> C | LOC_Os03g26260.1 | upstream_gene_variant ; 4127.0bp to feature; MODIFIER | silent_mutation | Average:41.23; most accessible tissue: Callus, score: 67.433 | N | N | N | N |
| vg0315011678 | CGGAGGTAGT -> C | LOC_Os03g26229.1 | downstream_gene_variant ; 3419.0bp to feature; MODIFIER | silent_mutation | Average:41.23; most accessible tissue: Callus, score: 67.433 | N | N | N | N |
| vg0315011678 | CGGAGGTAGT -> C | LOC_Os03g26250.1 | intron_variant ; MODIFIER | silent_mutation | Average:41.23; most accessible tissue: Callus, score: 67.433 | N | N | N | N |
| vg0315011678 | CGGAGGTAGT -> TGGAGGTAGT | LOC_Os03g26240.1 | upstream_gene_variant ; 2225.0bp to feature; MODIFIER | silent_mutation | Average:41.23; most accessible tissue: Callus, score: 67.433 | N | N | N | N |
| vg0315011678 | CGGAGGTAGT -> TGGAGGTAGT | LOC_Os03g26260.1 | upstream_gene_variant ; 4128.0bp to feature; MODIFIER | silent_mutation | Average:41.23; most accessible tissue: Callus, score: 67.433 | N | N | N | N |
| vg0315011678 | CGGAGGTAGT -> TGGAGGTAGT | LOC_Os03g26229.1 | downstream_gene_variant ; 3418.0bp to feature; MODIFIER | silent_mutation | Average:41.23; most accessible tissue: Callus, score: 67.433 | N | N | N | N |
| vg0315011678 | CGGAGGTAGT -> TGGAGGTAGT | LOC_Os03g26250.1 | intron_variant ; MODIFIER | silent_mutation | Average:41.23; most accessible tissue: Callus, score: 67.433 | N | N | N | N |