| Variant ID: vg1112795322 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 12795322 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCCATTGGCCCAATACAGGAGACGCAGCACCTTGCTTTTGTGATTGCGGCCAAACGAGATAGATTTCCGAGATGAGGCTGGATCCGTTGGAAGGAGGACT[T/C]
CGAGAGCTTTGCATCAAGTACTCACGGGCCCAAAACGGAGCACGTATGTAGATTTGGCGGCCGTTTGAAGTCAGCAATGTAACACGTGGCCGAATCAGAT
ATCTGATTCGGCCACGTGTTACATTGCTGACTTCAAACGGCCGCCAAATCTACATACGTGCTCCGTTTTGGGCCCGTGAGTACTTGATGCAAAGCTCTCG[A/G]
AGTCCTCCTTCCAACGGATCCAGCCTCATCTCGGAAATCTATCTCGTTTGGCCGCAATCACAAAAGCAAGGTGCTGCGTCTCCTGTATTGGGCCAATGGG
| 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 | 32.40% | 2.30% | 39.44% | 25.92% | NA |
| All Indica | 2759 | 3.20% | 0.10% | 58.97% | 37.80% | NA |
| All Japonica | 1512 | 87.60% | 6.70% | 1.46% | 4.17% | NA |
| Aus | 269 | 0.70% | 0.00% | 66.54% | 32.71% | NA |
| Indica I | 595 | 3.40% | 0.00% | 36.97% | 59.66% | NA |
| Indica II | 465 | 2.40% | 0.00% | 42.58% | 55.05% | NA |
| Indica III | 913 | 2.00% | 0.00% | 86.86% | 11.17% | NA |
| Indica Intermediate | 786 | 4.80% | 0.30% | 52.93% | 41.98% | NA |
| Temperate Japonica | 767 | 82.30% | 13.00% | 1.83% | 2.87% | NA |
| Tropical Japonica | 504 | 91.50% | 0.00% | 1.19% | 7.34% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.80% | 0.83% | 1.66% | NA |
| VI/Aromatic | 96 | 85.40% | 0.00% | 11.46% | 3.12% | NA |
| Intermediate | 90 | 37.80% | 3.30% | 27.78% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1112795322 | T -> DEL | N | N | silent_mutation | Average:10.993; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg1112795322 | T -> C | LOC_Os11g22310.1 | upstream_gene_variant ; 2012.0bp to feature; MODIFIER | silent_mutation | Average:10.993; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg1112795322 | T -> C | LOC_Os11g22330.1 | upstream_gene_variant ; 3351.0bp to feature; MODIFIER | silent_mutation | Average:10.993; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg1112795322 | T -> C | LOC_Os11g22320.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.993; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |