| Variant ID: vg0609018604 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9018604 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCAAGGGGTGTATGCAATTGAATTGGGTGCCAAGAGAGCCCCCTTGCAGCTGGTGGGGGAGTATTTATACTCCCACCCACCAAAACTAGCCGTTAGGGGC[G/A]
AAATCCCCAAACTTTGTGCTCTGCCGGTCTGACCGAAGGTATGTGGCCGGTCAGACCATGCTACTCTGCAACGGCTAGAAAACTAGCCGTTGAAGTGCTG
CAGCACTTCAACGGCTAGTTTTCTAGCCGTTGCAGAGTAGCATGGTCTGACCGGCCACATACCTTCGGTCAGACCGGCAGAGCACAAAGTTTGGGGATTT[C/T]
GCCCCTAACGGCTAGTTTTGGTGGGTGGGAGTATAAATACTCCCCCACCAGCTGCAAGGGGGCTCTCTTGGCACCCAATTCAATTGCATACACCCCTTGC
| 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 | 50.00% | 0.50% | 7.43% | 42.02% | NA |
| All Indica | 2759 | 59.00% | 0.90% | 4.97% | 35.09% | NA |
| All Japonica | 1512 | 44.60% | 0.00% | 8.86% | 46.49% | NA |
| Aus | 269 | 1.10% | 0.00% | 15.61% | 83.27% | NA |
| Indica I | 595 | 57.50% | 0.50% | 1.18% | 40.84% | NA |
| Indica II | 465 | 78.90% | 0.00% | 4.52% | 16.56% | NA |
| Indica III | 913 | 44.10% | 2.20% | 8.11% | 45.56% | NA |
| Indica Intermediate | 786 | 65.80% | 0.30% | 4.45% | 29.52% | NA |
| Temperate Japonica | 767 | 74.20% | 0.00% | 2.74% | 23.08% | NA |
| Tropical Japonica | 504 | 12.90% | 0.00% | 14.09% | 73.02% | NA |
| Japonica Intermediate | 241 | 17.00% | 0.00% | 17.43% | 65.56% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 31.25% | 59.38% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 8.89% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609018604 | G -> A | LOC_Os06g15880.1 | missense_variant ; p.Glu99Lys; MODERATE | nonsynonymous_codon ; E99K | Average:39.475; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 | unknown | unknown | TOLERATED | 0.39 |
| vg0609018604 | G -> DEL | LOC_Os06g15880.1 | N | frameshift_variant | Average:39.475; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 | N | N | N | N |