| Variant ID: vg1220960838 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960838 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AACCGTACTCTAACTGAGATGGTGAATGCCATGTTAGACACTGCGGGGCTTTCCAAGGAATGGTGGGGTGAGGCAGTTTTGACTGCTTGTCATGTCCTGA[A/C]
TAAAATTCCAATGAAGCATAAGGAAGTAACACCATTCGAGGAATGGGAAAGGAAGAAATTAAATCTCTCATACCTACGAACATGGGGCTGTTTGGCCAAG
CTTGGCCAAACAGCCCCATGTTCGTAGGTATGAGAGATTTAATTTCTTCCTTTCCCATTCCTCGAATGGTGTTACTTCCTTATGCTTCATTGGAATTTTA[T/G]
TCAGGACATGACAAGCAGTCAAAACTGCCTCACCCCACCATTCCTTGGAAAGCCCCGCAGTGTCTAACATGGCATTCACCATCTCAGTTAGAGTACGGTT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.40% | 0.40% | 0.89% | 40.27% | NA |
| All Indica | 2759 | 78.50% | 0.50% | 0.72% | 20.30% | NA |
| All Japonica | 1512 | 26.80% | 0.20% | 0.99% | 72.02% | NA |
| Aus | 269 | 50.20% | 0.70% | 1.86% | 47.21% | NA |
| Indica I | 595 | 62.70% | 0.30% | 0.84% | 36.13% | NA |
| Indica II | 465 | 79.10% | 0.00% | 0.22% | 20.65% | NA |
| Indica III | 913 | 88.20% | 0.20% | 0.66% | 10.95% | NA |
| Indica Intermediate | 786 | 78.90% | 1.10% | 1.02% | 18.96% | NA |
| Temperate Japonica | 767 | 10.60% | 0.00% | 0.78% | 88.66% | NA |
| Tropical Japonica | 504 | 47.60% | 0.60% | 1.39% | 50.40% | NA |
| Japonica Intermediate | 241 | 34.90% | 0.00% | 0.83% | 64.32% | NA |
| VI/Aromatic | 96 | 16.70% | 0.00% | 0.00% | 83.33% | NA |
| Intermediate | 90 | 43.30% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960838 | A -> C | LOC_Os12g34580.1 | missense_variant ; p.Asn741Thr; MODERATE | nonsynonymous_codon | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1220960838 | A -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |