| Variant ID: vg1221990146 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 21990146 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATCGGTCCCATGATCCCCAGCCGACCATTCCTCCTGCAATGGTGAGTCCGTCAGGAAACCGTAGCAGCTGCGCCTCAACGGGGCAGGTAGGATCACAGAG[C/T]
ATGGACGCCATGCAAACACAGGACGAATCGACCTGTCCCGTTGATGACATCACTCAGCGGACACCATGTGAGCTGCATATTCCTTTCAAGAACTTATCAA
TTGATAAGTTCTTGAAAGGAATATGCAGCTCACATGGTGTCCGCTGAGTGATGTCATCAACGGGACAGGTCGATTCGTCCTGTGTTTGCATGGCGTCCAT[G/A]
CTCTGTGATCCTACCTGCCCCGTTGAGGCGCAGCTGCTACGGTTTCCTGACGGACTCACCATTGCAGGAGGAATGGTCGGCTGGGGATCATGGGACCGAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.30% | 0.50% | 2.88% | 30.34% | NA |
| All Indica | 2759 | 54.40% | 0.00% | 2.57% | 43.02% | NA |
| All Japonica | 1512 | 91.30% | 0.00% | 0.40% | 8.33% | NA |
| Aus | 269 | 45.40% | 0.00% | 14.13% | 40.52% | NA |
| Indica I | 595 | 68.20% | 0.00% | 0.67% | 31.09% | NA |
| Indica II | 465 | 72.70% | 0.00% | 0.86% | 26.45% | NA |
| Indica III | 913 | 33.10% | 0.10% | 5.59% | 61.23% | NA |
| Indica Intermediate | 786 | 57.80% | 0.00% | 1.53% | 40.71% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.26% | 3.26% | NA |
| Tropical Japonica | 504 | 80.20% | 0.00% | 0.79% | 19.05% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 58.30% | 22.90% | 17.71% | 1.04% | NA |
| Intermediate | 90 | 83.30% | 0.00% | 4.44% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1221990146 | C -> DEL | N | N | silent_mutation | Average:11.452; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| vg1221990146 | C -> T | LOC_Os12g35980.1 | upstream_gene_variant ; 4934.0bp to feature; MODIFIER | silent_mutation | Average:11.452; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| vg1221990146 | C -> T | LOC_Os12g35970.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.452; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |