| Variant ID: vg0204059219 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 4059219 |
| Reference Allele: TTGGTGCAA | Alternative Allele: ATGGTGCAA,T |
| Primary Allele: TTGGTGCAA | Secondary Allele: ATGGTGCAA |
Inferred Ancestral Allele: Not determined.
TGCATGGCAGCATGGGAATGAAGGGCAGAAAAGTGGATAGGTAAACTTCCCTGGTGCTTTATTTGAAAGGAGAAACTTGATGAAACTTCATGTGAATTTG[TTGGTGCAA/ATGGTGCAA,T]
TTTAATTTGAATGCATATGCATGTGGATGCAACGCTTTTATTTTGTTAATTACCTCTAGTTGCTCATGTAGCCTTCTTTGCACCTCCATCTGCATTCTGA
TCAGAATGCAGATGGAGGTGCAAAGAAGGCTACATGAGCAACTAGAGGTAATTAACAAAATAAAAGCGTTGCATCCACATGCATATGCATTCAAATTAAA[TTGCACCAA/TTGCACCAT,A]
CAAATTCACATGAAGTTTCATCAAGTTTCTCCTTTCAAATAAAGCACCAGGGAAGTTTACCTATCCACTTTTCTGCCCTTCATTCCCATGCTGCCATGCA
| Populations | Population Size | Frequency of TTGGTGCAA(primary allele) | Frequency of ATGGTGCAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.00% | 41.40% | 0.08% | 0.00% | T: 0.59% |
| All Indica | 2759 | 35.60% | 64.40% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Aus | 269 | 37.90% | 51.30% | 1.12% | 0.00% | T: 9.67% |
| Indica I | 595 | 33.10% | 66.90% | 0.00% | 0.00% | NA |
| Indica II | 465 | 28.00% | 72.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 40.70% | 59.10% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 35.90% | 64.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 5.20% | 0.00% | 0.00% | T: 1.04% |
| Intermediate | 90 | 66.70% | 32.20% | 0.00% | 0.00% | T: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0204059219 | TTGGTGCAA -> T | LOC_Os02g07770.1 | intron_variant ; MODIFIER | silent_mutation | Average:42.858; most accessible tissue: Callus, score: 80.707 | N | N | N | N |
| vg0204059219 | TTGGTGCAA -> ATGGTGCAA | LOC_Os02g07770.1 | intron_variant ; MODIFIER | silent_mutation | Average:42.858; most accessible tissue: Callus, score: 80.707 | N | N | N | N |