| Variant ID: vg0607893790 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7893790 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCCCTCGCAGGTTCGTCTCTCACCCATCGTGGCTGTATTCATTCTCTCAACGCGAGTTTTCACTCACCCATCTTGTTCGTCTTCTGGTCTTTTCTTTTGT[T/C]
TCAGCGAGATCCCGTCGCGTCCCTCCCGCCATTCCAAGTCCGGCCAGTCTGAGGCCGAGGATCCGGCGACCGCAGAGGCCCGCAGGCGGCAAGCTGACCG
CGGTCAGCTTGCCGCCTGCGGGCCTCTGCGGTCGCCGGATCCTCGGCCTCAGACTGGCCGGACTTGGAATGGCGGGAGGGACGCGACGGGATCTCGCTGA[A/G]
ACAAAAGAAAAGACCAGAAGACGAACAAGATGGGTGAGTGAAAACTCGCGTTGAGAGAATGAATACAGCCACGATGGGTGAGAGACGAACCTGCGAGGGG
| 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 | 8.90% | 0.10% | 8.53% | 82.46% | NA |
| All Indica | 2759 | 3.50% | 0.20% | 12.40% | 83.87% | NA |
| All Japonica | 1512 | 20.20% | 0.00% | 0.99% | 78.77% | NA |
| Aus | 269 | 1.50% | 0.00% | 10.78% | 87.73% | NA |
| Indica I | 595 | 1.50% | 0.00% | 6.39% | 92.10% | NA |
| Indica II | 465 | 0.90% | 0.00% | 10.11% | 89.03% | NA |
| Indica III | 913 | 7.60% | 0.70% | 16.76% | 75.03% | NA |
| Indica Intermediate | 786 | 1.90% | 0.00% | 13.23% | 84.86% | NA |
| Temperate Japonica | 767 | 34.40% | 0.00% | 0.13% | 65.45% | NA |
| Tropical Japonica | 504 | 3.80% | 0.00% | 1.98% | 94.25% | NA |
| Japonica Intermediate | 241 | 9.50% | 0.00% | 1.66% | 88.80% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 7.29% | 90.62% | NA |
| Intermediate | 90 | 12.20% | 0.00% | 11.11% | 76.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607893790 | T -> C | LOC_Os06g14150.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893790 | T -> C | LOC_Os06g14140.1 | upstream_gene_variant ; 4052.0bp to feature; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893790 | T -> C | LOC_Os06g14160.1 | downstream_gene_variant ; 2689.0bp to feature; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893790 | T -> DEL | N | N | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |