| Variant ID: vg1120445550 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20445550 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTCCTAGATAGAGACGACTAAGAGATGGTATGCTCCCAAGTATTTGCAGGTCCCTCTCTTTCAGTGTGTCTAATTTGATAGTTAGATTGGAGAGGGTGGA[T/G]
AGGGAGACCATCCAGTTTGGCACTGCATGGATGGTGCTATTCCACATGCCAATGGAACAAAGCTGTTGAGGTCTAGGAGATGAATCATCACATGCAGAAT
ATTCTGCATGTGATGATTCATCTCCTAGACCTCAACAGCTTTGTTCCATTGGCATGTGGAATAGCACCATCCATGCAGTGCCAAACTGGATGGTCTCCCT[A/C]
TCCACCCTCTCCAATCTAACTATCAAATTAGACACACTGAAAGAGAGGGACCTGCAAATACTTGGGAGCATACCATCTCTTAGTCGTCTCTATCTAGGAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.90% | 0.20% | 1.23% | 20.65% | NA |
| All Indica | 2759 | 70.20% | 0.30% | 1.30% | 28.23% | NA |
| All Japonica | 1512 | 94.90% | 0.20% | 1.19% | 3.70% | NA |
| Aus | 269 | 53.50% | 0.00% | 1.49% | 44.98% | NA |
| Indica I | 595 | 52.80% | 0.00% | 1.34% | 45.88% | NA |
| Indica II | 465 | 79.60% | 0.00% | 2.15% | 18.28% | NA |
| Indica III | 913 | 70.00% | 0.70% | 1.53% | 27.82% | NA |
| Indica Intermediate | 786 | 78.10% | 0.10% | 0.51% | 21.25% | NA |
| Temperate Japonica | 767 | 96.30% | 0.10% | 2.22% | 1.30% | NA |
| Tropical Japonica | 504 | 90.70% | 0.40% | 0.20% | 8.73% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 0.00% | 12.50% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120445550 | T -> DEL | LOC_Os11g34880.1 | N | frameshift_variant | Average:44.69; most accessible tissue: Callus, score: 95.124 | N | N | N | N |
| vg1120445550 | T -> G | LOC_Os11g34880.1 | synonymous_variant ; p.Leu446Leu; LOW | synonymous_codon | Average:44.69; most accessible tissue: Callus, score: 95.124 | N | N | N | N |