| Variant ID: vg0128509385 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28509385 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GGTTTCGTAGGAAGCGGTTCGCGCCGTTTTTCCCACGACACGCTCCTGTCAGGTGCCGTTGTACGGCGGTGCCAGATTGGGGTGTGACATATATGAACGA[T/C]
GGGAGGCGCGTGATGGTGGCGGTGTCTAGGCCGAACCTGGGCAGCGTCGGCTGCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACGCCGGCGACAGG
CCTGTCGCCGGCGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGCAGCCGACGCTGCCCAGGTTCGGCCTAGACACCGCCACCATCACGCGCCTCCC[A/G]
TCGTTCATATATGTCACACCCCAATCTGGCACCGCCGTACAACGGCACCTGACAGGAGCGTGTCGTGGGAAAAACGGCGCGAACCGCTTCCTACGAAACC
| 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 | 25.00% | 0.10% | 9.44% | 65.38% | NA |
| All Indica | 2759 | 1.60% | 0.00% | 12.40% | 85.97% | NA |
| All Japonica | 1512 | 72.20% | 0.40% | 5.69% | 21.69% | NA |
| Aus | 269 | 1.90% | 0.00% | 2.60% | 95.54% | NA |
| Indica I | 595 | 1.80% | 0.00% | 3.70% | 94.45% | NA |
| Indica II | 465 | 2.40% | 0.00% | 3.44% | 94.19% | NA |
| Indica III | 913 | 0.80% | 0.00% | 28.81% | 70.43% | NA |
| Indica Intermediate | 786 | 1.90% | 0.10% | 5.22% | 92.75% | NA |
| Temperate Japonica | 767 | 92.80% | 0.00% | 0.65% | 6.52% | NA |
| Tropical Japonica | 504 | 33.10% | 1.20% | 14.88% | 50.79% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.00% | 2.49% | 9.13% | NA |
| VI/Aromatic | 96 | 14.60% | 0.00% | 0.00% | 85.42% | NA |
| Intermediate | 90 | 31.10% | 0.00% | 12.22% | 56.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509385 | T -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:21.355; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0128509385 | T -> C | LOC_Os01g49570.1 | synonymous_variant ; p.Pro63Pro; LOW | synonymous_codon | Average:21.355; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |