| Variant ID: vg1216387285 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16387285 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCTCTGTTCCTAGGACTGAATTTGAGTCCTTTGCATACTTTCCCGTAGCCATGGTGCTACCAAATATTGTAAGCATCTCACCATAGTGTGCAAGAGGTTT[G/A]
TTAAAATAATCAGCATCAGCCTTGTGATCCTTCGGTGAAACAAAATTTTTTTAAGTAAATGCAATAAAACAAATGAATGGAATAAAGCACTAGGTCAAGA
TCTTGACCTAGTGCTTTATTCCATTCATTTGTTTTATTGCATTTACTTAAAAAAATTTTGTTTCACCGAAGGATCACAAGGCTGATGCTGATTATTTTAA[C/T]
AAACCTCTTGCACACTATGGTGAGATGCTTACAATATTTGGTAGCACCATGGCTACGGGAAAGTATGCAAAGGACTCAAATTCAGTCCTAGGAACAGAGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 74.00% | 0.40% | 14.94% | 10.66% | NA |
| All Indica | 2759 | 64.80% | 0.60% | 21.20% | 13.41% | NA |
| All Japonica | 1512 | 85.50% | 0.00% | 6.61% | 7.87% | NA |
| Aus | 269 | 95.20% | 0.00% | 1.49% | 3.35% | NA |
| Indica I | 595 | 49.90% | 1.30% | 40.84% | 7.90% | NA |
| Indica II | 465 | 61.30% | 0.00% | 21.08% | 17.63% | NA |
| Indica III | 913 | 77.20% | 0.30% | 7.45% | 15.01% | NA |
| Indica Intermediate | 786 | 63.60% | 0.80% | 22.39% | 13.23% | NA |
| Temperate Japonica | 767 | 94.30% | 0.00% | 3.78% | 1.96% | NA |
| Tropical Japonica | 504 | 71.80% | 0.00% | 10.91% | 17.26% | NA |
| Japonica Intermediate | 241 | 86.30% | 0.00% | 6.64% | 7.05% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 77.80% | 0.00% | 16.67% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216387285 | G -> DEL | LOC_Os12g27800.1 | N | frameshift_variant | Average:5.247; most accessible tissue: Callus, score: 10.072 | N | N | N | N |
| vg1216387285 | G -> A | LOC_Os12g27800.1 | synonymous_variant ; p.Asn421Asn; LOW | synonymous_codon | Average:5.247; most accessible tissue: Callus, score: 10.072 | N | N | N | N |