| Variant ID: vg1101255944 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1255944 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAAACTATGCAGCAGGCTATAAAAAATAAGCCAAAGGATTTTGACCCATCTGATTGGCAATGGCTTGTCCAGGAGCATTTTTATAGCAAAGATTTTATTG[T/A]
AAGTGATGATGTCCCCTCTCTTTCCAGTATGTTCTATGCATTTTACTTGACTTATATTTGCCCAAAATGAGTCCGTTTGTTAACTAAATACAGGCAATGA
TCATTGCCTGTATTTAGTTAACAAACGGACTCATTTTGGGCAAATATAAGTCAAGTAAAATGCATAGAACATACTGGAAAGAGAGGGGACATCATCACTT[A/T]
CAATAAAATCTTTGCTATAAAAATGCTCCTGGACAAGCCATTGCCAATCAGATGGGTCAAAATCCTTTGGCTTATTTTTTATAGCCTGCTGCATAGTTTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.50% | 1.80% | 5.42% | 29.35% | NA |
| All Indica | 2759 | 45.10% | 2.50% | 6.52% | 45.85% | NA |
| All Japonica | 1512 | 97.60% | 0.00% | 0.40% | 2.05% | NA |
| Aus | 269 | 62.10% | 4.10% | 14.13% | 19.70% | NA |
| Indica I | 595 | 14.30% | 0.00% | 10.08% | 75.63% | NA |
| Indica II | 465 | 40.90% | 4.50% | 6.02% | 48.60% | NA |
| Indica III | 913 | 65.10% | 3.30% | 4.16% | 27.49% | NA |
| Indica Intermediate | 786 | 47.70% | 2.40% | 6.87% | 43.00% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 0.78% | 1.43% | NA |
| Tropical Japonica | 504 | 97.80% | 0.00% | 0.00% | 2.18% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.00% | 0.00% | 3.73% | NA |
| VI/Aromatic | 96 | 60.40% | 1.00% | 22.92% | 15.62% | NA |
| Intermediate | 90 | 62.20% | 1.10% | 11.11% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101255944 | T -> A | LOC_Os11g03340.1 | splice_donor_variant&intron_variant ; HIGH | splice_donor_variant | Average:5.151; most accessible tissue: Minghui63 young leaf, score: 8.301 | N | N | N | N |
| vg1101255944 | T -> DEL | LOC_Os11g03340.1 | N | splice_donor_variant | Average:5.151; most accessible tissue: Minghui63 young leaf, score: 8.301 | N | N | N | N |