| Variant ID: vg0137500585 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 37500585 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGGCGCACCCCAATGAACATCTCGCACAGATGCGCGAAGATGGCCAATGTCATCACCGCGTTGGGGGTGAGGTGCGCCATCTGGAGATCGTAGAACTCCA[G/A]
AACATCCATGAAGAAAGAAGAAAATGGTGGAACCAGCCCTGCCATTGCAAAGGGGAGAAAGAAGACGAACCGCCCCGGGTAGTCTGGCGCCGGGCGTCCC
GGGACGCCCGGCGCCAGACTACCCGGGGCGGTTCGTCTTCTTTCTCCCCTTTGCAATGGCAGGGCTGGTTCCACCATTTTCTTCTTTCTTCATGGATGTT[C/T]
TGGAGTTCTACGATCTCCAGATGGCGCACCTCACCCCCAACGCGGTGATGACATTGGCCATCTTCGCGCATCTGTGCGAGATGTTCATTGGGGTGCGCCC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.20% | 3.70% | 0.19% | 63.97% | NA |
| All Indica | 2759 | 2.20% | 0.00% | 0.14% | 97.64% | NA |
| All Japonica | 1512 | 86.40% | 11.40% | 0.13% | 2.05% | NA |
| Aus | 269 | 0.70% | 0.00% | 1.12% | 98.14% | NA |
| Indica I | 595 | 1.30% | 0.00% | 0.34% | 98.32% | NA |
| Indica II | 465 | 1.30% | 0.00% | 0.00% | 98.71% | NA |
| Indica III | 913 | 0.90% | 0.00% | 0.00% | 99.12% | NA |
| Indica Intermediate | 786 | 5.00% | 0.00% | 0.25% | 94.78% | NA |
| Temperate Japonica | 767 | 83.30% | 14.70% | 0.26% | 1.69% | NA |
| Tropical Japonica | 504 | 96.00% | 1.40% | 0.00% | 2.58% | NA |
| Japonica Intermediate | 241 | 76.30% | 21.60% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 63.30% | 1.10% | 0.00% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137500585 | G -> A | LOC_Os01g64610.1 | synonymous_variant ; p.Leu79Leu; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0137500585 | G -> DEL | LOC_Os01g64610.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |