| Variant ID: vg0915031255 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 15031255 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCCGCTTCATGCCGGAGTCCGCCACCGGTCGGGAGATAGTGATGCTGGGCGAGGGGCGCCCGGCACCAGACTACCCGGGGCGGTCCATCTTCTTCCTCCC[C/T]
TTCGCAATGGCTGGGCTGGTCCCGCCATTTTCTTCTTTCTTCATGGATGTCCTGGAGTTCTACGATCTCCAGATGGCGCACCTCACCCCTAATGCGGTGA
TCACCGCATTAGGGGTGAGGTGCGCCATCTGGAGATCGTAGAACTCCAGGACATCCATGAAGAAAGAAGAAAATGGCGGGACCAGCCCAGCCATTGCGAA[G/A]
GGGAGGAAGAAGATGGACCGCCCCGGGTAGTCTGGTGCCGGGCGCCCCTCGCCCAGCATCACTATCTCCCGACCGGTGGCGGACTCCGGCATGAAGCGGC
| 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 | 13.00% | 0.10% | 0.93% | 85.95% | NA |
| All Indica | 2759 | 0.30% | 0.10% | 0.58% | 99.02% | NA |
| All Japonica | 1512 | 38.80% | 0.00% | 0.00% | 61.24% | NA |
| Aus | 269 | 0.00% | 0.40% | 10.41% | 89.22% | NA |
| Indica I | 595 | 0.20% | 0.00% | 0.17% | 99.66% | NA |
| Indica II | 465 | 0.90% | 0.00% | 1.29% | 97.85% | NA |
| Indica III | 913 | 0.00% | 0.30% | 0.66% | 99.01% | NA |
| Indica Intermediate | 786 | 0.30% | 0.10% | 0.38% | 99.24% | NA |
| Temperate Japonica | 767 | 66.40% | 0.00% | 0.00% | 33.64% | NA |
| Tropical Japonica | 504 | 3.80% | 0.00% | 0.00% | 96.23% | NA |
| Japonica Intermediate | 241 | 24.10% | 0.00% | 0.00% | 75.93% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 0.00% | 92.71% | NA |
| Intermediate | 90 | 16.70% | 0.00% | 0.00% | 83.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0915031255 | C -> DEL | LOC_Os09g25110.1 | N | frameshift_variant | Average:10.189; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0915031255 | C -> T | LOC_Os09g25110.1 | synonymous_variant ; p.Pro61Pro; LOW | synonymous_codon | Average:10.189; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |