| Variant ID: vg0143002415 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 43002415 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AAGCTGCCACACCGGAATCGGAGGGGTTCCAGGTCCATGCCTCCTCCTTACGAGCCACTCGGTCCGCGAGCTGAAAAAGCTCCGCGGTAGTCTGGGGCTC[T/C]
TTGGAGGCGATCTTTTCGAGCATGCGGTTGTGCCGCACACCCCCCCTGAACGCGTAAATCACCGCGTGTGCAGGGATGCATGGTATGGTGTTGCGGACTT
AAGTCCGCAACACCATACCATGCATCCCTGCACACGCGGTGATTTACGCGTTCAGGGGGGGTGTGCGGCACAACCGCATGCTCGAAAAGATCGCCTCCAA[A/G]
GAGCCCCAGACTACCGCGGAGCTTTTTCAGCTCGCGGACCGAGTGGCTCGTAAGGAGGAGGCATGGACCTGGAACCCCTCCGATTCCGGTGTGGCAGCTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 10.40% | 0.90% | 7.28% | 81.38% | NA |
| All Indica | 2759 | 2.00% | 1.40% | 8.19% | 88.44% | NA |
| All Japonica | 1512 | 27.90% | 0.10% | 3.77% | 68.25% | NA |
| Aus | 269 | 0.40% | 0.00% | 16.73% | 82.90% | NA |
| Indica I | 595 | 2.70% | 0.20% | 3.19% | 93.95% | NA |
| Indica II | 465 | 1.30% | 0.40% | 7.53% | 90.75% | NA |
| Indica III | 913 | 1.80% | 3.20% | 12.38% | 82.69% | NA |
| Indica Intermediate | 786 | 2.20% | 0.80% | 7.51% | 89.57% | NA |
| Temperate Japonica | 767 | 38.90% | 0.10% | 2.74% | 58.28% | NA |
| Tropical Japonica | 504 | 20.40% | 0.00% | 4.17% | 75.40% | NA |
| Japonica Intermediate | 241 | 8.70% | 0.00% | 6.22% | 85.06% | NA |
| VI/Aromatic | 96 | 1.00% | 2.10% | 10.42% | 86.46% | NA |
| Intermediate | 90 | 15.60% | 2.20% | 6.67% | 75.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0143002415 | T -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:5.247; most accessible tissue: Zhenshan97 young leaf, score: 9.167 | N | N | N | N |
| vg0143002415 | T -> C | LOC_Os01g74230.1 | synonymous_variant ; p.Lys299Lys; LOW | synonymous_codon | Average:5.247; most accessible tissue: Zhenshan97 young leaf, score: 9.167 | N | N | N | N |