| Variant ID: vg0522747460 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 22747460 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GCCCGTCTCACCACCTCCGCCGCGGCGCGCCCACCTCGTGGCACGCCATCCGCGCACACACGCACGCTGTCGTCCTGGCCCCCCACGCGCGCACCCGATC[C/G]
GCCCGCGCGTCCGCCCGCGGGAAGAGAGAAGGGGGCGATCGATCGATCGATCGCGCCGGGGCGCGCGCGCGCGTGGAGGGGGGGAAGGAGAGGGCGATGG
CCATCGCCCTCTCCTTCCCCCCCTCCACGCGCGCGCGCGCCCCGGCGCGATCGATCGATCGATCGCCCCCTTCTCTCTTCCCGCGGGCGGACGCGCGGGC[G/C]
GATCGGGTGCGCGCGTGGGGGGCCAGGACGACAGCGTGCGTGTGTGCGCGGATGGCGTGCCACGAGGTGGGCGCGCCGCGGCGGAGGTGGTGAGACGGGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.50% | 5.40% | 6.67% | 3.43% | NA |
| All Indica | 2759 | 87.40% | 9.10% | 2.21% | 1.27% | NA |
| All Japonica | 1512 | 76.00% | 0.00% | 16.34% | 7.67% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 67.10% | 32.10% | 0.67% | 0.17% | NA |
| Indica II | 465 | 88.80% | 1.30% | 5.81% | 4.09% | NA |
| Indica III | 913 | 97.30% | 1.30% | 0.88% | 0.55% | NA |
| Indica Intermediate | 786 | 90.60% | 5.30% | 2.80% | 1.27% | NA |
| Temperate Japonica | 767 | 58.40% | 0.00% | 27.51% | 14.08% | NA |
| Tropical Japonica | 504 | 97.80% | 0.00% | 2.18% | 0.00% | NA |
| Japonica Intermediate | 241 | 86.30% | 0.00% | 10.37% | 3.32% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 85.60% | 3.30% | 6.67% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0522747460 | C -> DEL | N | N | silent_mutation | Average:73.451; most accessible tissue: Zhenshan97 flower, score: 85.807 | N | N | N | N |
| vg0522747460 | C -> G | LOC_Os05g38770.1 | 5_prime_UTR_variant ; 262.0bp to feature; MODIFIER | silent_mutation | Average:73.451; most accessible tissue: Zhenshan97 flower, score: 85.807 | N | N | N | N |
| vg0522747460 | C -> G | LOC_Os05g38760.1 | upstream_gene_variant ; 3008.0bp to feature; MODIFIER | silent_mutation | Average:73.451; most accessible tissue: Zhenshan97 flower, score: 85.807 | N | N | N | N |
| vg0522747460 | C -> G | LOC_Os05g38780.1 | upstream_gene_variant ; 4083.0bp to feature; MODIFIER | silent_mutation | Average:73.451; most accessible tissue: Zhenshan97 flower, score: 85.807 | N | N | N | N |