| Variant ID: vg0125112043 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 25112043 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCACGTCATCGGCAGACAACCGAGCTCCCACGTTGCATCTGCTTCCGGCGGAGTGGAGGTAGATATG[A/G]
CCCATCCCATCGGAGGGTCATTCGGACAGCAGCCATTGCAAATCTTCACCCATTAATGAAGGAATGACAGGGAGATCCCCTGTGTCAGGCGAGTGATGAC
GTCATCACTCGCCTGACACAGGGGATCTCCCTGTCATTCCTTCATTAATGGGTGAAGATTTGCAATGGCTGCTGTCCGAATGACCCTCCGATGGGATGGG[T/C]
CATATCTACCTCCACTCCGCCGGAAGCAGATGCAACGTGGGAGCTCGGTTGTCTGCCGATGACGTGACCGGCGTCAGACCAGTCACAGACCGGTCATTCT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.90% | 0.40% | 5.82% | 42.93% | NA |
| All Indica | 2759 | 39.60% | 0.70% | 8.99% | 50.78% | NA |
| All Japonica | 1512 | 74.80% | 0.00% | 0.93% | 24.27% | NA |
| Aus | 269 | 16.00% | 0.00% | 1.49% | 82.53% | NA |
| Indica I | 595 | 34.30% | 0.00% | 14.79% | 50.92% | NA |
| Indica II | 465 | 60.90% | 0.20% | 4.95% | 33.98% | NA |
| Indica III | 913 | 30.30% | 1.60% | 8.00% | 60.02% | NA |
| Indica Intermediate | 786 | 41.70% | 0.30% | 8.14% | 49.87% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.13% | 1.56% | NA |
| Tropical Japonica | 504 | 44.40% | 0.00% | 1.59% | 53.97% | NA |
| Japonica Intermediate | 241 | 63.50% | 0.00% | 2.07% | 34.44% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 1.04% | 12.50% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 8.89% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0125112043 | A -> G | LOC_Os01g43830.1 | synonymous_variant ; p.Gly2Gly; LOW | synonymous_codon | Average:6.081; most accessible tissue: Callus, score: 10.3 | N | N | N | N |
| vg0125112043 | A -> DEL | LOC_Os01g43830.1 | N | frameshift_variant | Average:6.081; most accessible tissue: Callus, score: 10.3 | N | N | N | N |