| Variant ID: vg1218480424 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18480424 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AATCCGCCGATTCCTCTCTTTCCAAATTTCCCAGACGACTAACAGAATGAGCGATCGAAGTCCTTTTTTCGGGACACTAGGCGTGTTTGCAATGTTCTCC[C/T]
ACCACTGTTTGACTGACTGGGCTTCCTCCCATTCCGTTGGGTCCATCTGCTGATAGCCCACCCATGCAGAGACGAGGTGCCAGATCCTCTTGGTGTATCT
AGATACACCAAGAGGATCTGGCACCTCGTCTCTGCATGGGTGGGCTATCAGCAGATGGACCCAACGGAATGGGAGGAAGCCCAGTCAGTCAAACAGTGGT[G/A]
GGAGAACATTGCAAACACGCCTAGTGTCCCGAAAAAAGGACTTCGATCGCTCATTCTGTTAGTCGTCTGGGAAATTTGGAAAGAGAGGAATCGGCGGATT
| 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 | 36.70% | 0.30% | 13.03% | 49.94% | NA |
| All Indica | 2759 | 30.50% | 0.60% | 17.62% | 51.29% | NA |
| All Japonica | 1512 | 39.60% | 0.00% | 3.37% | 57.08% | NA |
| Aus | 269 | 73.60% | 0.00% | 17.10% | 9.29% | NA |
| Indica I | 595 | 15.30% | 0.70% | 19.83% | 64.20% | NA |
| Indica II | 465 | 21.70% | 0.00% | 16.13% | 62.15% | NA |
| Indica III | 913 | 46.00% | 0.80% | 18.07% | 35.16% | NA |
| Indica Intermediate | 786 | 29.30% | 0.60% | 16.28% | 53.82% | NA |
| Temperate Japonica | 767 | 60.90% | 0.00% | 1.30% | 37.81% | NA |
| Tropical Japonica | 504 | 12.30% | 0.00% | 6.55% | 81.15% | NA |
| Japonica Intermediate | 241 | 28.60% | 0.00% | 3.32% | 68.05% | NA |
| VI/Aromatic | 96 | 49.00% | 0.00% | 22.92% | 28.12% | NA |
| Intermediate | 90 | 54.40% | 0.00% | 12.22% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480424 | C -> DEL | LOC_Os12g30780.1 | N | frameshift_variant | Average:6.828; most accessible tissue: Minghui63 young leaf, score: 11.521 | N | N | N | N |
| vg1218480424 | C -> T | LOC_Os12g30780.1 | stop_gained ; p.Trp196*; HIGH | stop_gained | Average:6.828; most accessible tissue: Minghui63 young leaf, score: 11.521 | N | N | N | N |