| Variant ID: vg1120445551 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20445551 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCCTAGATAGAGACGACTAAGAGATGGTATGCTCCCAAGTATTTGCAGGTCCCTCTCTTTCAGTGTGTCTAATTTGATAGTTAGATTGGAGAGGGTGGAT[A/T]
GGGAGACCATCCAGTTTGGCACTGCATGGATGGTGCTATTCCACATGCCAATGGAACAAAGCTGTTGAGGTCTAGGAGATGAATCATCACATGCAGAATC
GATTCTGCATGTGATGATTCATCTCCTAGACCTCAACAGCTTTGTTCCATTGGCATGTGGAATAGCACCATCCATGCAGTGCCAAACTGGATGGTCTCCC[T/A]
ATCCACCCTCTCCAATCTAACTATCAAATTAGACACACTGAAAGAGAGGGACCTGCAAATACTTGGGAGCATACCATCTCTTAGTCGTCTCTATCTAGGA
| 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 | 83.60% | 0.10% | 0.42% | 15.83% | NA |
| All Indica | 2759 | 78.80% | 0.00% | 0.65% | 20.59% | NA |
| All Japonica | 1512 | 96.90% | 0.20% | 0.00% | 2.91% | NA |
| Aus | 269 | 55.00% | 0.00% | 0.74% | 44.24% | NA |
| Indica I | 595 | 77.60% | 0.00% | 1.01% | 21.34% | NA |
| Indica II | 465 | 80.20% | 0.00% | 1.08% | 18.71% | NA |
| Indica III | 913 | 77.40% | 0.00% | 0.55% | 22.02% | NA |
| Indica Intermediate | 786 | 80.30% | 0.00% | 0.25% | 19.47% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 91.10% | 0.60% | 0.00% | 8.33% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 0.00% | 11.46% | NA |
| Intermediate | 90 | 91.10% | 2.20% | 0.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120445551 | A -> T | LOC_Os11g34880.1 | missense_variant ; p.Leu446Gln; MODERATE | nonsynonymous_codon ; L446Q | Average:44.743; most accessible tissue: Callus, score: 95.124 | unknown | unknown | DELETERIOUS | 0.01 |
| vg1120445551 | A -> DEL | LOC_Os11g34880.1 | N | frameshift_variant | Average:44.743; most accessible tissue: Callus, score: 95.124 | N | N | N | N |