| Variant ID: vg1220960847 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960847 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )
CTAACTGAGATGGTGAATGCCATGTTAGACACTGCGGGGCTTTCCAAGGAATGGTGGGGTGAGGCAGTTTTGACTGCTTGTCATGTCCTGAATAAAATTC[C/T]
AATGAAGCATAAGGAAGTAACACCATTCGAGGAATGGGAAAGGAAGAAATTAAATCTCTCATACCTACGAACATGGGGCTGTTTGGCCAAGGTAAATGTA
TACATTTACCTTGGCCAAACAGCCCCATGTTCGTAGGTATGAGAGATTTAATTTCTTCCTTTCCCATTCCTCGAATGGTGTTACTTCCTTATGCTTCATT[G/A]
GAATTTTATTCAGGACATGACAAGCAGTCAAAACTGCCTCACCCCACCATTCCTTGGAAAGCCCCGCAGTGTCTAACATGGCATTCACCATCTCAGTTAG
| 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 | 58.90% | 0.20% | 0.70% | 40.20% | NA |
| All Indica | 2759 | 78.80% | 0.40% | 0.51% | 20.33% | NA |
| All Japonica | 1512 | 27.20% | 0.00% | 0.79% | 72.02% | NA |
| Aus | 269 | 52.40% | 0.00% | 1.86% | 45.72% | NA |
| Indica I | 595 | 63.00% | 0.00% | 0.67% | 36.30% | NA |
| Indica II | 465 | 78.90% | 0.00% | 0.43% | 20.65% | NA |
| Indica III | 913 | 88.20% | 0.70% | 0.22% | 10.95% | NA |
| Indica Intermediate | 786 | 79.80% | 0.50% | 0.76% | 18.96% | NA |
| Temperate Japonica | 767 | 10.60% | 0.00% | 0.78% | 88.66% | NA |
| Tropical Japonica | 504 | 48.60% | 0.00% | 0.99% | 50.40% | NA |
| Japonica Intermediate | 241 | 35.30% | 0.00% | 0.41% | 64.32% | NA |
| VI/Aromatic | 96 | 16.70% | 0.00% | 0.00% | 83.33% | NA |
| Intermediate | 90 | 45.60% | 0.00% | 2.22% | 52.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960847 | C -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg1220960847 | C -> T | LOC_Os12g34580.1 | missense_variant ; p.Pro744Leu; MODERATE | nonsynonymous_codon ; P744L | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | unknown | unknown | DELETERIOUS | 0.02 |