| Variant ID: vg0131449053 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 31449053 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACTTGCCGGTTGGGCGTTCCCTGTTGGGAGCGCCGGCCTCGTCCTTTTTGCCTCCCGCAGGCCTCCCCTTTCGGGTGGCCCGCGAAGCGCCCTCGACGGC[G/A]
AGGACATGACCCTCGTCGTCGGTATGGGCTGACCTCTTCTTCCTCCTCCTGTCACGCCGCCCTATCTGAGCGGCGGATCCGGGGGCGGCCGAAGCTGCCA
TGGCAGCTTCGGCCGCCCCCGGATCCGCCGCTCAGATAGGGCGGCGTGACAGGAGGAGGAAGAAGAGGTCAGCCCATACCGACGACGAGGGTCATGTCCT[C/T]
GCCGTCGAGGGCGCTTCGCGGGCCACCCGAAAGGGGAGGCCTGCGGGAGGCAAAAAGGACGAGGCCGGCGCTCCCAACAGGGAACGCCCAACCGGCAAGT
| 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 | 31.30% | 0.20% | 2.48% | 66.04% | NA |
| All Indica | 2759 | 2.70% | 0.00% | 4.02% | 93.29% | NA |
| All Japonica | 1512 | 82.50% | 0.50% | 0.26% | 16.73% | NA |
| Aus | 269 | 0.70% | 0.00% | 0.37% | 98.88% | NA |
| Indica I | 595 | 3.70% | 0.00% | 3.70% | 92.61% | NA |
| Indica II | 465 | 1.10% | 0.00% | 3.23% | 95.70% | NA |
| Indica III | 913 | 0.90% | 0.00% | 4.82% | 94.30% | NA |
| Indica Intermediate | 786 | 5.00% | 0.00% | 3.82% | 91.22% | NA |
| Temperate Japonica | 767 | 87.70% | 0.00% | 0.13% | 12.13% | NA |
| Tropical Japonica | 504 | 88.30% | 1.60% | 0.40% | 9.72% | NA |
| Japonica Intermediate | 241 | 53.50% | 0.00% | 0.41% | 46.06% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 72.20% | 0.00% | 1.11% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0131449053 | G -> A | LOC_Os01g54660.1 | synonymous_variant ; p.Leu440Leu; LOW | synonymous_codon | Average:17.923; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 | N | N | N | N |
| vg0131449053 | G -> DEL | LOC_Os01g54660.1 | N | frameshift_variant | Average:17.923; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 | N | N | N | N |