| Variant ID: vg1101691860 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1691860 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AACAACTACCGCTCACTTCTTCCCGCCATTTCCTCTCAACCCATCAAACTCACACACCCATTTCTTCCTTCTACCAAAAATTCTCTCTCCGATCCGTGCC[T/C]
CTCCGTCGCCGGAGCAGGCACGCGCGAATCCCACCGACGCCATGGGCCAGTGCTGCACGGGTGGCGGGAAGGCCGTCGCCGGCGACGAGGCAGAGCCGGG
CCCGGCTCTGCCTCGTCGCCGGCGACGGCCTTCCCGCCACCCGTGCAGCACTGGCCCATGGCGTCGGTGGGATTCGCGCGTGCCTGCTCCGGCGACGGAG[A/G]
GGCACGGATCGGAGAGAGAATTTTTGGTAGAAGGAAGAAATGGGTGTGTGAGTTTGATGGGTTGAGAGGAAATGGCGGGAAGAAGTGAGCGGTAGTTGTT
| 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 | 99.40% | 0.60% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 91.10% | 8.60% | 0.37% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 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 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1101691860 | T -> C | LOC_Os11g04150.1 | upstream_gene_variant ; 3761.0bp to feature; MODIFIER | silent_mutation | Average:68.171; most accessible tissue: Zhenshan97 root, score: 82.361 | N | N | N | N |
| vg1101691860 | T -> C | LOC_Os11g04170.1 | upstream_gene_variant ; 1.0bp to feature; MODIFIER | silent_mutation | Average:68.171; most accessible tissue: Zhenshan97 root, score: 82.361 | N | N | N | N |
| vg1101691860 | T -> C | LOC_Os11g04160.1 | downstream_gene_variant ; 520.0bp to feature; MODIFIER | silent_mutation | Average:68.171; most accessible tissue: Zhenshan97 root, score: 82.361 | N | N | N | N |
| vg1101691860 | T -> C | LOC_Os11g04174.1 | downstream_gene_variant ; 2612.0bp to feature; MODIFIER | silent_mutation | Average:68.171; most accessible tissue: Zhenshan97 root, score: 82.361 | N | N | N | N |
| vg1101691860 | T -> C | LOC_Os11g04180.1 | downstream_gene_variant ; 4567.0bp to feature; MODIFIER | silent_mutation | Average:68.171; most accessible tissue: Zhenshan97 root, score: 82.361 | N | N | N | N |
| vg1101691860 | T -> C | LOC_Os11g04160-LOC_Os11g04170 | intergenic_region ; MODIFIER | silent_mutation | Average:68.171; most accessible tissue: Zhenshan97 root, score: 82.361 | N | N | N | N |