| Variant ID: vg1218480780 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18480780 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGGGTTTCCAAATCAAGGAATTGAAGTTTGTACTCGGCGCCCCGCAGCACTGCGCATGGTAAGCCGAGGAGGCCGTGTAGTGCCCGTTGTTTGTGAACTT[C/T]
CAAGTAATCTGATCCGGTTCTCCAACATCTAAGTGCACATTTCGGACCGCTTCCCACAGTGCGACTAGCTGTTCGACGAGGTCGACTGCGATAGATGATT
AATCATCTATCGCAGTCGACCTCGTCGAACAGCTAGTCGCACTGTGGGAAGCGGTCCGAAATGTGCACTTAGATGTTGGAGAACCGGATCAGATTACTTG[G/A]
AAGTTCACAAACAACGGGCACTACACGGCCTCCTCGGCTTACCATGCGCAGTGCTGCGGGGCGCCGAGTACAAACTTCAATTCCTTGATTTGGAAACCCT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.70% | 0.40% | 13.35% | 52.58% | NA |
| All Indica | 2759 | 25.80% | 0.60% | 18.41% | 55.20% | NA |
| All Japonica | 1512 | 39.20% | 0.00% | 3.11% | 57.74% | NA |
| Aus | 269 | 72.90% | 0.70% | 16.36% | 10.04% | NA |
| Indica I | 595 | 12.90% | 0.70% | 16.97% | 69.41% | NA |
| Indica II | 465 | 15.90% | 0.00% | 19.78% | 64.30% | NA |
| Indica III | 913 | 39.40% | 0.90% | 19.82% | 39.87% | NA |
| Indica Intermediate | 786 | 25.40% | 0.60% | 17.05% | 56.87% | NA |
| Temperate Japonica | 767 | 61.00% | 0.00% | 1.04% | 37.94% | NA |
| Tropical Japonica | 504 | 10.90% | 0.00% | 6.75% | 82.34% | NA |
| Japonica Intermediate | 241 | 28.60% | 0.00% | 2.07% | 69.29% | NA |
| VI/Aromatic | 96 | 47.90% | 0.00% | 20.83% | 31.25% | NA |
| Intermediate | 90 | 51.10% | 0.00% | 13.33% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480780 | C -> DEL | LOC_Os12g30780.1 | N | frameshift_variant | Average:6.619; most accessible tissue: Callus, score: 17.876 | N | N | N | N |
| vg1218480780 | C -> T | LOC_Os12g30780.1 | stop_gained ; p.Trp77*; HIGH | stop_gained | Average:6.619; most accessible tissue: Callus, score: 17.876 | N | N | N | N |