| Variant ID: vg1225601711 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25601711 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGGCGTCCTCTCATGTATGATGCCATGTTCCTCACAGAATAAGTCAAACTCGTTCGAGAAAAACTCTCCACCACGATCAGACCTAAGCCTTTTTATCTTT[C/T]
TGTCAAGTTGATTTTCAACTTCTGCCTTATAAATTTTAAAATAGTCTAGAGCCTCGTCTTTCGTTTTCAACAAGTACACATAGCAAAATCTAGTAGCATC
GATGCTACTAGATTTTGCTATGTGTACTTGTTGAAAACGAAAGACGAGGCTCTAGACTATTTTAAAATTTATAAGGCAGAAGTTGAAAATCAACTTGACA[G/A]
AAAGATAAAAAGGCTTAGGTCTGATCGTGGTGGAGAGTTTTTCTCGAACGAGTTTGACTTATTCTGTGAGGAACATGGCATCATACATGAGAGGACGCCT
| 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 | 55.20% | 0.10% | 11.81% | 32.92% | NA |
| All Indica | 2759 | 42.40% | 0.20% | 12.07% | 45.38% | NA |
| All Japonica | 1512 | 87.20% | 0.00% | 12.43% | 0.33% | NA |
| Aus | 269 | 1.50% | 0.00% | 5.58% | 92.94% | NA |
| Indica I | 595 | 86.40% | 0.00% | 3.03% | 10.59% | NA |
| Indica II | 465 | 19.10% | 0.00% | 12.47% | 68.39% | NA |
| Indica III | 913 | 28.90% | 0.50% | 18.95% | 51.59% | NA |
| Indica Intermediate | 786 | 38.40% | 0.00% | 10.69% | 50.89% | NA |
| Temperate Japonica | 767 | 87.50% | 0.00% | 12.13% | 0.39% | NA |
| Tropical Japonica | 504 | 96.00% | 0.00% | 3.97% | 0.00% | NA |
| Japonica Intermediate | 241 | 68.00% | 0.00% | 31.12% | 0.83% | NA |
| VI/Aromatic | 96 | 60.40% | 0.00% | 11.46% | 28.12% | NA |
| Intermediate | 90 | 63.30% | 0.00% | 12.22% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225601711 | C -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:9.765; most accessible tissue: Zhenshan97 flag leaf, score: 18.943 | N | N | N | N |
| vg1225601711 | C -> T | LOC_Os12g41280.1 | missense_variant ; p.Arg551Lys; MODERATE | nonsynonymous_codon ; R551K | Average:9.765; most accessible tissue: Zhenshan97 flag leaf, score: 18.943 | unknown | unknown | TOLERATED | 0.31 |