| Variant ID: vg1216387327 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 16387327 |
| Reference Allele: A | Alternative Allele: AT |
| Primary Allele: A | Secondary Allele: AT |
Inferred Ancestral Allele: Not determined.
CCGTAGCCATGGTGCTACCAAATATTGTAAGCATCTCACCATAGTGTGCAAGAGGTTTGTTAAAATAATCAGCATCAGCCTTGTGATCCTTCGGTGAAAC[A/AT]
AAATTTTTTTAAGTAAATGCAATAAAACAAATGAATGGAATAAAGCACTAGGTCAAGACATTTACCTCAATATAGCCATTGTAGTGCTCATCATCAAGAG
CTCTTGATGATGAGCACTACAATGGCTATATTGAGGTAAATGTCTTGACCTAGTGCTTTATTCCATTCATTTGTTTTATTGCATTTACTTAAAAAAATTT[T/AT]
GTTTCACCGAAGGATCACAAGGCTGATGCTGATTATTTTAACAAACCTCTTGCACACTATGGTGAGATGCTTACAATATTTGGTAGCACCATGGCTACGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.50% | 0.10% | 11.09% | 61.32% | NA |
| All Indica | 2759 | 9.20% | 0.10% | 11.92% | 78.69% | NA |
| All Japonica | 1512 | 60.80% | 0.00% | 5.95% | 33.20% | NA |
| Aus | 269 | 24.50% | 0.00% | 21.56% | 53.90% | NA |
| Indica I | 595 | 4.70% | 0.20% | 9.92% | 85.21% | NA |
| Indica II | 465 | 11.60% | 0.00% | 14.84% | 73.55% | NA |
| Indica III | 913 | 8.90% | 0.30% | 10.84% | 79.96% | NA |
| Indica Intermediate | 786 | 11.70% | 0.00% | 12.98% | 75.32% | NA |
| Temperate Japonica | 767 | 88.40% | 0.00% | 3.39% | 8.21% | NA |
| Tropical Japonica | 504 | 15.90% | 0.00% | 9.13% | 75.00% | NA |
| Japonica Intermediate | 241 | 67.20% | 0.00% | 7.47% | 25.31% | NA |
| VI/Aromatic | 96 | 24.00% | 0.00% | 41.67% | 34.38% | NA |
| Intermediate | 90 | 40.00% | 0.00% | 7.78% | 52.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216387327 | A -> DEL | N | N | silent_mutation | Average:4.716; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1216387327 | A -> AT | LOC_Os12g27810.1 | upstream_gene_variant ; 4097.0bp to feature; MODIFIER | silent_mutation | Average:4.716; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1216387327 | A -> AT | LOC_Os12g27790.1 | downstream_gene_variant ; 3306.0bp to feature; MODIFIER | silent_mutation | Average:4.716; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1216387327 | A -> AT | LOC_Os12g27800.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.716; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |