| Variant ID: vg0221509787 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21509787 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTCAAGTCCGCAACACCATACCAAGCATCCCTGCACACGCGGTGATCTACGCGTTCAGGGGGGGTGTGCGGCACAACCGCATGCTCGAAAAGATCGCCTC[C/T]
AAAGAGCCCCAGACTACCGCGGAGCTTTTTCAGCTCGTGGACCGAGTGGCTCGCAAGGAGGAGGCCTGGACTTGGAACCCCTCCGGTTCCAGTGTGGCAG
CTGCCACACTGGAACCGGAGGGGTTCCAAGTCCAGGCCTCCTCCTTGCGAGCCACTCGGTCCACGAGCTGAAAAAGCTCCGCGGTAGTCTGGGGCTCTTT[G/A]
GAGGCGATCTTTTCGAGCATGCGGTTGTGCCGCACACCCCCCCTGAACGCGTAGATCACCGCGTGTGCAGGGATGCTTGGTATGGTGTTGCGGACTTGAC
| 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 | 33.60% | 0.20% | 2.58% | 63.69% | NA |
| All Indica | 2759 | 2.40% | 0.00% | 1.27% | 96.30% | NA |
| All Japonica | 1512 | 91.10% | 0.50% | 5.29% | 3.04% | NA |
| Aus | 269 | 0.70% | 0.00% | 1.49% | 97.77% | NA |
| Indica I | 595 | 2.40% | 0.00% | 0.67% | 96.97% | NA |
| Indica II | 465 | 2.60% | 0.00% | 0.86% | 96.56% | NA |
| Indica III | 913 | 1.90% | 0.00% | 0.99% | 97.15% | NA |
| Indica Intermediate | 786 | 3.10% | 0.00% | 2.29% | 94.66% | NA |
| Temperate Japonica | 767 | 88.50% | 1.00% | 9.13% | 1.30% | NA |
| Tropical Japonica | 504 | 93.30% | 0.00% | 0.99% | 5.75% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.00% | 2.07% | 2.90% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 56.70% | 0.00% | 3.33% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221509787 | C -> T | LOC_Os02g35800.1 | synonymous_variant ; p.Ser375Ser; LOW | synonymous_codon | Average:6.501; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg0221509787 | C -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:6.501; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |