| Variant ID: vg1221990654 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 21990654 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGTGCACCATCTCCTCCGGCTCCGCCATCTCCTCCTCAGGATCCTGCACCGTCTCCTCCTCATGCTCCGCCAGCACCGTCTCCACCTCAGGCTCCAGCAT[C/T]
GACTCCTCCTCAAGATCCTGCACCGACTCCTCCTCGTGCTCCTACACCTACTCCCCCGCAAGCTCCTCTTCCGGCACCTTCAAAGTCAAGGGCCCCCCCA
TGGGGGGGCCCTTGACTTTGAAGGTGCCGGAAGAGGAGCTTGCGGGGGAGTAGGTGTAGGAGCACGAGGAGGAGTCGGTGCAGGATCTTGAGGAGGAGTC[G/A]
ATGCTGGAGCCTGAGGTGGAGACGGTGCTGGCGGAGCATGAGGAGGAGACGGTGCAGGATCCTGAGGAGGAGATGGCGGAGCCGGAGGAGATGGTGCACG
| 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 | 66.10% | 0.50% | 2.64% | 30.72% | NA |
| All Indica | 2759 | 54.20% | 0.00% | 2.61% | 43.17% | NA |
| All Japonica | 1512 | 91.20% | 0.00% | 0.20% | 8.60% | NA |
| Aus | 269 | 45.00% | 0.00% | 10.78% | 44.24% | NA |
| Indica I | 595 | 68.10% | 0.00% | 0.84% | 31.09% | NA |
| Indica II | 465 | 72.70% | 0.00% | 0.86% | 26.45% | NA |
| Indica III | 913 | 32.60% | 0.10% | 5.37% | 61.88% | NA |
| Indica Intermediate | 786 | 57.80% | 0.00% | 1.78% | 40.46% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.00% | 3.52% | NA |
| Tropical Japonica | 504 | 80.00% | 0.00% | 0.60% | 19.44% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 58.30% | 22.90% | 17.71% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1221990654 | C -> DEL | LOC_Os12g35970.1 | N | frameshift_variant | Average:15.948; most accessible tissue: Minghui63 young leaf, score: 40.718 | N | N | N | N |
| vg1221990654 | C -> T | LOC_Os12g35970.1 | missense_variant ; p.Ser184Leu; MODERATE | nonsynonymous_codon ; S184L | Average:15.948; most accessible tissue: Minghui63 young leaf, score: 40.718 | unknown | unknown | DELETERIOUS | 0.04 |