| Variant ID: vg0609018613 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9018613 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GTATGCAATTGAATTGGGTGCCAAGAGAGCCCCCTTGCAGCTGGTGGGGGAGTATTTATACTCCCACCCACCAAAACTAGCCGTTAGGGGCGAAATCCCC[A/C]
AACTTTGTGCTCTGCCGGTCTGACCGAAGGTATGTGGCCGGTCAGACCATGCTACTCTGCAACGGCTAGAAAACTAGCCGTTGAAGTGCTGTCAGAGGGC
GCCCTCTGACAGCACTTCAACGGCTAGTTTTCTAGCCGTTGCAGAGTAGCATGGTCTGACCGGCCACATACCTTCGGTCAGACCGGCAGAGCACAAAGTT[T/G]
GGGGATTTCGCCCCTAACGGCTAGTTTTGGTGGGTGGGAGTATAAATACTCCCCCACCAGCTGCAAGGGGGCTCTCTTGGCACCCAATTCAATTGCATAC
| 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 | 47.80% | 0.20% | 2.58% | 49.41% | NA |
| All Indica | 2759 | 58.20% | 0.20% | 1.85% | 39.72% | NA |
| All Japonica | 1512 | 39.90% | 0.30% | 3.04% | 56.75% | NA |
| Aus | 269 | 1.10% | 0.00% | 0.37% | 98.51% | NA |
| Indica I | 595 | 57.30% | 0.20% | 0.17% | 42.35% | NA |
| Indica II | 465 | 78.50% | 0.00% | 0.00% | 21.51% | NA |
| Indica III | 913 | 42.90% | 0.30% | 5.48% | 51.26% | NA |
| Indica Intermediate | 786 | 64.80% | 0.10% | 0.00% | 35.11% | NA |
| Temperate Japonica | 767 | 73.10% | 0.10% | 0.65% | 26.08% | NA |
| Tropical Japonica | 504 | 3.40% | 0.20% | 5.56% | 90.87% | NA |
| Japonica Intermediate | 241 | 10.40% | 1.20% | 5.39% | 82.99% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 22.92% | 73.96% | NA |
| Intermediate | 90 | 46.70% | 1.10% | 2.22% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609018613 | A -> C | LOC_Os06g15880.1 | missense_variant ; p.Lys102Gln; MODERATE | nonsynonymous_codon ; K102Q | Average:40.181; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 | unknown | unknown | TOLERATED | 0.60 |
| vg0609018613 | A -> DEL | LOC_Os06g15880.1 | N | frameshift_variant | Average:40.181; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 | N | N | N | N |