| Variant ID: vg1220960849 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960849 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AACTGAGATGGTGAATGCCATGTTAGACACTGCGGGGCTTTCCAAGGAATGGTGGGGTGAGGCAGTTTTGACTGCTTGTCATGTCCTGAATAAAATTCCA[A/T]
TGAAGCATAAGGAAGTAACACCATTCGAGGAATGGGAAAGGAAGAAATTAAATCTCTCATACCTACGAACATGGGGCTGTTTGGCCAAGGTAAATGTACC
GGTACATTTACCTTGGCCAAACAGCCCCATGTTCGTAGGTATGAGAGATTTAATTTCTTCCTTTCCCATTCCTCGAATGGTGTTACTTCCTTATGCTTCA[T/A]
TGGAATTTTATTCAGGACATGACAAGCAGTCAAAACTGCCTCACCCCACCATTCCTTGGAAAGCCCCGCAGTGTCTAACATGGCATTCACCATCTCAGTT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.60% | 0.30% | 1.42% | 41.62% | NA |
| All Indica | 2759 | 77.90% | 0.10% | 0.91% | 21.06% | NA |
| All Japonica | 1512 | 22.10% | 0.80% | 2.51% | 74.60% | NA |
| Aus | 269 | 52.00% | 0.00% | 0.74% | 47.21% | NA |
| Indica I | 595 | 60.20% | 0.00% | 2.18% | 37.65% | NA |
| Indica II | 465 | 78.90% | 0.00% | 0.22% | 20.86% | NA |
| Indica III | 913 | 88.10% | 0.20% | 0.33% | 11.39% | NA |
| Indica Intermediate | 786 | 79.00% | 0.10% | 1.02% | 19.85% | NA |
| Temperate Japonica | 767 | 8.00% | 0.30% | 2.22% | 89.57% | NA |
| Tropical Japonica | 504 | 38.70% | 1.80% | 3.37% | 56.15% | NA |
| Japonica Intermediate | 241 | 32.40% | 0.40% | 1.66% | 65.56% | NA |
| VI/Aromatic | 96 | 12.50% | 0.00% | 1.04% | 86.46% | NA |
| Intermediate | 90 | 44.40% | 1.10% | 1.11% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960849 | A -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg1220960849 | A -> T | LOC_Os12g34580.1 | missense_variant ; p.Met745Leu; MODERATE | nonsynonymous_codon ; M745L | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | unknown | unknown | TOLERATED | 0.11 |