| Variant ID: vg0404368253 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 4368253 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TAGGGTTTTTGGTTCTTTTGATCCGTGCGGATCTTGTGCTTTTCTCTCTTTGGATTTCTTTTCCCGAACCGATCTAAGCCCTAGGATCGCTCTGATACCA[A/T]
TGTTATACTTTGCACTAGGATCACCTAGGTTAGATCTAGTCGGGTGGTTCTATTTGGGATTGAGGTTTGAACTATAGAGATTGAAAACGGGAGAGGGTTT
AAACCCTCTCCCGTTTTCAATCTCTATAGTTCAAACCTCAATCCCAAATAGAACCACCCGACTAGATCTAACCTAGGTGATCCTAGTGCAAAGTATAACA[T/A]
TGGTATCAGAGCGATCCTAGGGCTTAGATCGGTTCGGGAAAAGAAATCCAAAGAGAGAAAAGCACAAGATCCGCACGGATCAAAAGAACCAAAAACCCTA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.10% | 0.30% | 20.86% | 49.75% | NA |
| All Indica | 2759 | 19.40% | 0.40% | 29.29% | 50.85% | NA |
| All Japonica | 1512 | 51.90% | 0.00% | 5.29% | 42.86% | NA |
| Aus | 269 | 10.00% | 0.00% | 23.79% | 66.17% | NA |
| Indica I | 595 | 9.10% | 0.00% | 49.58% | 41.34% | NA |
| Indica II | 465 | 23.20% | 0.20% | 28.17% | 48.39% | NA |
| Indica III | 913 | 22.50% | 1.10% | 18.18% | 58.27% | NA |
| Indica Intermediate | 786 | 21.50% | 0.10% | 27.48% | 50.89% | NA |
| Temperate Japonica | 767 | 87.40% | 0.00% | 0.91% | 11.73% | NA |
| Tropical Japonica | 504 | 10.30% | 0.00% | 10.32% | 79.37% | NA |
| Japonica Intermediate | 241 | 25.70% | 0.00% | 8.71% | 65.56% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 17.71% | 75.00% | NA |
| Intermediate | 90 | 25.60% | 0.00% | 18.89% | 55.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0404368253 | A -> DEL | N | N | silent_mutation | Average:6.391; most accessible tissue: Callus, score: 9.548 | N | N | N | N |
| vg0404368253 | A -> T | LOC_Os04g08210.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.391; most accessible tissue: Callus, score: 9.548 | N | N | N | N |