| Variant ID: vg1109788305 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9788305 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CATGGTCTCCGACCGGAGCACCAGGTCGGAGCTCATCTGCGGGTACGACGACTTGTCCCGGAGCAGCGCCCCGAGGTACGGCGGCACGGCGTCGTGGCGC[C/T]
CCTCCACCACCTCCCTCGCCTCGATCTTGACTTTCTTTAGCACGGCGACGTCGTCGTGCGCCAGCACCAGCGCCAGCGCCAGGGACGACCTCACGTCGCC
GGCGACGTGAGGTCGTCCCTGGCGCTGGCGCTGGTGCTGGCGCACGACGACGTCGCCGTGCTAAAGAAAGTCAAGATCGAGGCGAGGGAGGTGGTGGAGG[G/A]
GCGCCACGACGCCGTGCCGCCGTACCTCGGGGCGCTGCTCCGGGACAAGTCGTCGTACCCGCAGATGAGCTCCGACCTGGTGCTCCGGTCGGAGACCATG
| 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 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 94.50% | 5.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109788305 | C -> T | LOC_Os11g17580.1 | missense_variant ; p.Gly137Glu; MODERATE | N | Average:74.972; most accessible tissue: Zhenshan97 young leaf, score: 86.542 | N | N | N | N |
| vg1109788305 | C -> T | LOC_Os11g17570.1 | downstream_gene_variant ; 2804.0bp to feature; MODIFIER | N | Average:74.972; most accessible tissue: Zhenshan97 young leaf, score: 86.542 | N | N | N | N |