| Variant ID: vg1220960803 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960803 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATTCACCCCAATCAAATGGGGTGGCCGAAAGAAAGAACCGTACTCTAACTGAGATGGTGAATGCCATGTTAGACACTGCGGGGCTTTCCAAGGAATGGTG[G/A]
GGTGAGGCAGTTTTGACTGCTTGTCATGTCCTGAATAAAATTCCAATGAAGCATAAGGAAGTAACACCATTCGAGGAATGGGAAAGGAAGAAATTAAATC
GATTTAATTTCTTCCTTTCCCATTCCTCGAATGGTGTTACTTCCTTATGCTTCATTGGAATTTTATTCAGGACATGACAAGCAGTCAAAACTGCCTCACC[C/T]
CACCATTCCTTGGAAAGCCCCGCAGTGTCTAACATGGCATTCACCATCTCAGTTAGAGTACGGTTCTTTCTTTCGGCCACCCCATTTGATTGGGGTGAAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.60% | 0.70% | 1.10% | 40.65% | NA |
| All Indica | 2759 | 78.60% | 0.50% | 0.58% | 20.33% | NA |
| All Japonica | 1512 | 23.70% | 1.10% | 1.98% | 73.15% | NA |
| Aus | 269 | 51.30% | 0.70% | 0.74% | 47.21% | NA |
| Indica I | 595 | 62.00% | 0.70% | 1.01% | 36.30% | NA |
| Indica II | 465 | 78.70% | 0.40% | 0.22% | 20.65% | NA |
| Indica III | 913 | 88.30% | 0.40% | 0.33% | 10.95% | NA |
| Indica Intermediate | 786 | 79.90% | 0.40% | 0.76% | 18.96% | NA |
| Temperate Japonica | 767 | 10.40% | 0.00% | 0.26% | 89.31% | NA |
| Tropical Japonica | 504 | 40.10% | 3.20% | 4.56% | 52.18% | NA |
| Japonica Intermediate | 241 | 32.00% | 0.40% | 2.07% | 65.56% | NA |
| VI/Aromatic | 96 | 14.60% | 1.00% | 1.04% | 83.33% | NA |
| Intermediate | 90 | 44.40% | 0.00% | 3.33% | 52.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960803 | G -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg1220960803 | G -> A | LOC_Os12g34580.1 | stop_gained ; p.Trp729*; HIGH | stop_gained | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |