| Variant ID: vg0609018524 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9018524 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGACAACTTGACTCTTGGCTAATCAACCCTCTAACATACTAGATGGATGAACACAAAGCTCAAATGAGTGTGAGAGAGGTGCAAGGGGTGTATGCAATTG[A/T]
ATTGGGTGCCAAGAGAGCCCCCTTGCAGCTGGTGGGGGAGTATTTATACTCCCACCCACCAAAACTAGCCGTTAGGGGCGAAATCCCCAAACTTTGTGCT
AGCACAAAGTTTGGGGATTTCGCCCCTAACGGCTAGTTTTGGTGGGTGGGAGTATAAATACTCCCCCACCAGCTGCAAGGGGGCTCTCTTGGCACCCAAT[T/A]
CAATTGCATACACCCCTTGCACCTCTCTCACACTCATTTGAGCTTTGTGTTCATCCATCTAGTATGTTAGAGGGTTGATTAGCCAAGAGTCAAGTTGTCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.30% | 0.20% | 2.16% | 3.39% | NA |
| All Indica | 2759 | 99.50% | 0.00% | 0.22% | 0.33% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.07% | NA |
| Aus | 269 | 9.30% | 2.60% | 34.57% | 53.53% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 98.20% | 0.00% | 0.76% | 1.02% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 1.00% | 2.08% | 3.12% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 1.11% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609018524 | A -> T | LOC_Os06g15880.1 | missense_variant ; p.Glu72Val; MODERATE | nonsynonymous_codon ; E72V | Average:35.172; most accessible tissue: Zhenshan97 flag leaf, score: 81.008 | unknown | unknown | TOLERATED | 0.20 |
| vg0609018524 | A -> DEL | LOC_Os06g15880.1 | N | frameshift_variant | Average:35.172; most accessible tissue: Zhenshan97 flag leaf, score: 81.008 | N | N | N | N |