| Variant ID: vg1220960818 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960818 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ATGGGGTGGCCGAAAGAAAGAACCGTACTCTAACTGAGATGGTGAATGCCATGTTAGACACTGCGGGGCTTTCCAAGGAATGGTGGGGTGAGGCAGTTTT[G/C]
ACTGCTTGTCATGTCCTGAATAAAATTCCAATGAAGCATAAGGAAGTAACACCATTCGAGGAATGGGAAAGGAAGAAATTAAATCTCTCATACCTACGAA
TTCGTAGGTATGAGAGATTTAATTTCTTCCTTTCCCATTCCTCGAATGGTGTTACTTCCTTATGCTTCATTGGAATTTTATTCAGGACATGACAAGCAGT[C/G]
AAAACTGCCTCACCCCACCATTCCTTGGAAAGCCCCGCAGTGTCTAACATGGCATTCACCATCTCAGTTAGAGTACGGTTCTTTCTTTCGGCCACCCCAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.60% | 0.40% | 1.44% | 41.56% | NA |
| All Indica | 2759 | 78.10% | 0.10% | 0.83% | 20.95% | NA |
| All Japonica | 1512 | 21.60% | 1.10% | 2.58% | 74.80% | NA |
| Aus | 269 | 52.40% | 0.00% | 1.49% | 46.10% | NA |
| Indica I | 595 | 61.30% | 0.00% | 1.34% | 37.31% | NA |
| Indica II | 465 | 78.70% | 0.00% | 0.43% | 20.86% | NA |
| Indica III | 913 | 88.00% | 0.10% | 0.55% | 11.39% | NA |
| Indica Intermediate | 786 | 79.00% | 0.30% | 1.02% | 19.72% | NA |
| Temperate Japonica | 767 | 8.00% | 0.40% | 1.96% | 89.70% | NA |
| Tropical Japonica | 504 | 37.70% | 2.20% | 3.57% | 56.55% | NA |
| Japonica Intermediate | 241 | 31.10% | 0.80% | 2.49% | 65.56% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 0.00% | 86.46% | NA |
| Intermediate | 90 | 44.40% | 0.00% | 2.22% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960818 | G -> C | LOC_Os12g34580.1 | missense_variant ; p.Leu734Phe; MODERATE | nonsynonymous_codon ; L734F | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | unknown | unknown | DELETERIOUS | 0.03 |
| vg1220960818 | G -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:8.83; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |