| Variant ID: vg1113567918 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 13567918 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAAAGTCCTGGCAGTATTTCCAGTCAAAATAAAAAAGTTTGACCAGGCCTTGTGCGACCTTGGAGCCAGTGTCAGCGTCATGCCAAAAGACGTCTTCGAC[A/T]
AGCTCAACTTCACGGTGTTGGCGCCAACACCGATGCCCCATCAATTGGCTAACTCGTCAGTCTGTTACCCGGCAGAGATAGCGGAGGATGTGCCAGTCAA
TTGACTGGCACATCCTCCGCTATCTCTGCCGGGTAACAGACTGACGAGTTAGCCAATTGATGGGGCATCGGTGTTGGCGCCAACACCGTGAAGTTGAGCT[T/A]
GTCGAAGACGTCTTTTGGCATGACGCTGACACTGGCTCCAAGGTCGCACAAGGCCTGGTCAAACTTTTTTATTTTGACTGGAAATACTGCCAGGACTTTG
| 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 | 99.50% | 0.50% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 99.40% | 0.60% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.20% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.00% | 1.90% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.30% | 0.13% | 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 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1113567918 | A -> T | LOC_Os11g23950.1 | stop_gained ; p.Lys8*; HIGH | stop_gained | Average:32.624; most accessible tissue: Minghui63 flag leaf, score: 48.324 | N | N | N | N |