| Variant ID: vg0142999885 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 42999885 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGGTCGTCAGGGGCCTTAGGCCTCCGTTCGGCTCGGGGGCCTCTTCTCCCTGCTCTTTCCCGGGTCGAGTCAGCACAGGGTTAGCCTCGGGGTCAAAGGG[C/T]
GATAGGTGCGGCCTTCCCACAGTGGCCTCAGGGCCTTCCTGGGGGTCGGGGGCTCCTAGCACCGTCTGACAAGCGGGCAGAGGGCCAACTCCGGTCGTCG
CGACGACCGGAGTTGGCCCTCTGCCCGCTTGTCAGACGGTGCTAGGAGCCCCCGACCCCCAGGAAGGCCCTGAGGCCACTGTGGGAAGGCCGCACCTATC[G/A]
CCCTTTGACCCCGAGGCTAACCCTGTGCTGACTCGACCCGGGAAAGAGCAGGGAGAAGAGGCCCCCGAGCCGAACGGAGGCCTAAGGCCCCTGACGACCG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 7.30% | 0.20% | 3.49% | 89.00% | NA |
| All Indica | 2759 | 1.10% | 0.30% | 3.26% | 95.40% | NA |
| All Japonica | 1512 | 20.10% | 0.00% | 2.12% | 77.78% | NA |
| Aus | 269 | 0.70% | 0.00% | 14.87% | 84.39% | NA |
| Indica I | 595 | 0.30% | 0.00% | 1.18% | 98.49% | NA |
| Indica II | 465 | 0.90% | 0.00% | 1.72% | 97.42% | NA |
| Indica III | 913 | 1.40% | 0.70% | 5.15% | 92.77% | NA |
| Indica Intermediate | 786 | 1.30% | 0.30% | 3.56% | 94.91% | NA |
| Temperate Japonica | 767 | 37.80% | 0.00% | 1.56% | 60.63% | NA |
| Tropical Japonica | 504 | 0.80% | 0.00% | 1.59% | 97.62% | NA |
| Japonica Intermediate | 241 | 4.10% | 0.00% | 4.98% | 90.87% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 2.08% | 97.92% | NA |
| Intermediate | 90 | 12.20% | 1.10% | 1.11% | 85.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0142999885 | C -> T | LOC_Os01g74230.1 | synonymous_variant ; p.Ser1039Ser; LOW | synonymous_codon | Average:4.687; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |
| vg0142999885 | C -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:4.687; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |