| Variant ID: vg0609018551 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9018551 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCTCTAACATACTAGATGGATGAACACAAAGCTCAAATGAGTGTGAGAGAGGTGCAAGGGGTGTATGCAATTGAATTGGGTGCCAAGAGAGCCCCCTTGC[A/T]
GCTGGTGGGGGAGTATTTATACTCCCACCCACCAAAACTAGCCGTTAGGGGCGAAATCCCCAAACTTTGTGCTCTGCCGGTCTGACCGAAGGTATGTGGC
GCCACATACCTTCGGTCAGACCGGCAGAGCACAAAGTTTGGGGATTTCGCCCCTAACGGCTAGTTTTGGTGGGTGGGAGTATAAATACTCCCCCACCAGC[T/A]
GCAAGGGGGCTCTCTTGGCACCCAATTCAATTGCATACACCCCTTGCACCTCTCTCACACTCATTTGAGCTTTGTGTTCATCCATCTAGTATGTTAGAGG
| 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 | 93.70% | 0.50% | 1.46% | 4.36% | NA |
| All Indica | 2759 | 99.20% | 0.20% | 0.14% | 0.43% | NA |
| All Japonica | 1512 | 98.70% | 0.90% | 0.26% | 0.13% | NA |
| Aus | 269 | 8.90% | 1.10% | 21.56% | 68.40% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.30% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 98.10% | 0.10% | 0.38% | 1.40% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 98.60% | 1.20% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 95.90% | 2.90% | 0.83% | 0.41% | NA |
| VI/Aromatic | 96 | 90.60% | 2.10% | 2.08% | 5.21% | NA |
| Intermediate | 90 | 94.40% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0609018551 | A -> T | LOC_Os06g15880.1 | missense_variant ; p.Gln81Leu; MODERATE | nonsynonymous_codon ; Q81L | Average:37.722; most accessible tissue: Zhenshan97 flag leaf, score: 83.994 | unknown | unknown | TOLERATED | 0.35 |
| vg0609018551 | A -> DEL | LOC_Os06g15880.1 | N | frameshift_variant | Average:37.722; most accessible tissue: Zhenshan97 flag leaf, score: 83.994 | N | N | N | N |