| Variant ID: vg0108238993 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 8238993 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TATGCTGCCGTTGTTGGGCGTCTACGTCTTCACCGACCGGCTCGCCTTCGTCGCCGCCGACTGGTGTCCACGCCTGCACGGCTGGCCTATTATGCCGCCG[C/T]
TGTTGGGCGCCTACGTCTTCACCGACCGGCTCGCCTTCGCCGCCGCCGACTGGTGTCCTCGCCTGCACGGCTGGCCTATTATGCCGCCGTTGTTGGGCGC
GCGCCCAACAACGGCGGCATAATAGGCCAGCCGTGCAGGCGAGGACACCAGTCGGCGGCGGCGAAGGCGAGCCGGTCGGTGAAGACGTAGGCGCCCAACA[G/A]
CGGCGGCATAATAGGCCAGCCGTGCAGGCGTGGACACCAGTCGGCGGCGACGAAGGCGAGCCGGTCGGTGAAGACGTAGACGCCCAACAACGGCAGCATA
| 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 | 98.10% | 0.00% | 0.95% | 0.89% | NA |
| All Indica | 2759 | 98.20% | 0.00% | 0.51% | 1.27% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.13% | 0.20% | NA |
| Aus | 269 | 88.80% | 0.40% | 10.78% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.00% | 0.00% | 0.50% | NA |
| Indica II | 465 | 93.30% | 0.00% | 1.29% | 5.38% | NA |
| Indica III | 913 | 99.80% | 0.10% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.20% | 0.00% | 0.89% | 0.89% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 0.00% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0108238993 | C -> T | LOC_Os01g14730.1 | synonymous_variant ; p.Leu64Leu; LOW | synonymous_codon | Average:46.361; most accessible tissue: Zhenshan97 flag leaf, score: 65.82 | N | N | N | N |
| vg0108238993 | C -> DEL | LOC_Os01g14730.1 | N | frameshift_variant | Average:46.361; most accessible tissue: Zhenshan97 flag leaf, score: 65.82 | N | N | N | N |