| Variant ID: vg1221989802 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 21989802 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TATTCTCGTAAATCATATCTATTGCTTAAATGTAGTTCTTTTCTTTACCTTCTTGGTGATCATTTATGGTTTGGCAAGCAATAGGAATCATAACAACCAG[C/T]
ATGATGCAAAAGTTTTAAAAAGTTCGAAATTTTAGTGATTTTTATTGTTGGGAATTTTTAGGATGTTACAGGTGATTCCTTGGAAGATTGGTTTCAAGGA
TCCTTGAAACCAATCTTCCAAGGAATCACCTGTAACATCCTAAAAATTCCCAACAATAAAAATCACTAAAATTTCGAACTTTTTAAAACTTTTGCATCAT[G/A]
CTGGTTGTTATGATTCCTATTGCTTGCCAAACCATAAATGATCACCAAGAAGGTAAAGAAAAGAACTACATTTAAGCAATAGATATGATTTACGAGAATA
| 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 | 66.80% | 0.40% | 3.49% | 29.33% | NA |
| All Indica | 2759 | 55.00% | 0.00% | 4.02% | 40.96% | NA |
| All Japonica | 1512 | 90.10% | 1.10% | 0.13% | 8.66% | NA |
| Aus | 269 | 46.10% | 0.00% | 11.90% | 42.01% | NA |
| Indica I | 595 | 68.60% | 0.00% | 1.18% | 30.25% | NA |
| Indica II | 465 | 73.10% | 0.00% | 1.29% | 25.59% | NA |
| Indica III | 913 | 34.00% | 0.00% | 8.21% | 57.83% | NA |
| Indica Intermediate | 786 | 58.40% | 0.10% | 2.93% | 38.55% | NA |
| Temperate Japonica | 767 | 96.60% | 0.00% | 0.00% | 3.39% | NA |
| Tropical Japonica | 504 | 79.40% | 0.60% | 0.20% | 19.84% | NA |
| Japonica Intermediate | 241 | 91.70% | 5.80% | 0.41% | 2.07% | NA |
| VI/Aromatic | 96 | 82.30% | 0.00% | 16.67% | 1.04% | NA |
| Intermediate | 90 | 83.30% | 0.00% | 4.44% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1221989802 | C -> DEL | N | N | silent_mutation | Average:10.282; most accessible tissue: Minghui63 root, score: 17.665 | N | N | N | N |
| vg1221989802 | C -> T | LOC_Os12g35970.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.282; most accessible tissue: Minghui63 root, score: 17.665 | N | N | N | N |