| Variant ID: vg0420969506 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 20969506 |
| Reference Allele: CTG | Alternative Allele: C |
| Primary Allele: CTG | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TGTACTATCATATTTAGTGATCACTCAGCATGTGGATTTTATATGTAGTATGGGAACTGATAAAGAAATTCTTTTCAGTGTATTTTTTTCTTTTCTTACT[CTG/C]
TGGAATTATGCAGTTCCTTTATTTGCTACATAATACTGCTGCAAATATCTGTTGCACTATCTTACTGCAGAGCTCATGTGATAGGCATGCACACTGGATG
CATCCAGTGTGCATGCCTATCACATGAGCTCTGCAGTAAGATAGTGCAACAGATATTTGCAGCAGTATTATGTAGCAAATAAAGGAACTGCATAATTCCA[CAG/G]
AGTAAGAAAAGAAAAAAATACACTGAAAAGAATTTCTTTATCAGTTCCCATACTACATATAAAATCCACATGCTGAGTGATCACTAAATATGATAGTACA
| Populations | Population Size | Frequency of CTG(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.70% | 0.60% | 2.29% | 40.39% | NA |
| All Indica | 2759 | 40.20% | 0.00% | 3.15% | 56.58% | NA |
| All Japonica | 1512 | 90.60% | 1.90% | 0.40% | 7.14% | NA |
| Aus | 269 | 24.90% | 0.00% | 1.49% | 73.61% | NA |
| Indica I | 595 | 77.80% | 0.00% | 0.67% | 21.51% | NA |
| Indica II | 465 | 17.20% | 0.20% | 2.80% | 79.78% | NA |
| Indica III | 913 | 34.20% | 0.00% | 5.48% | 60.35% | NA |
| Indica Intermediate | 786 | 32.40% | 0.00% | 2.54% | 65.01% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 75.40% | 5.60% | 1.19% | 17.86% | NA |
| Japonica Intermediate | 241 | 92.90% | 0.00% | 0.00% | 7.05% | NA |
| VI/Aromatic | 96 | 66.70% | 0.00% | 10.42% | 22.92% | NA |
| Intermediate | 90 | 75.60% | 1.10% | 1.11% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420969506 | CTG -> C | LOC_Os04g34650.1 | upstream_gene_variant ; 4839.0bp to feature; MODIFIER | silent_mutation | Average:4.444; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0420969506 | CTG -> C | LOC_Os04g34670.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.444; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0420969506 | CTG -> DEL | N | N | silent_mutation | Average:4.444; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |