| Variant ID: vg0607893783 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7893783 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AACCGACCCCCTCGCAGGTTCGTCTCTCACCCATCGTGGCTGTATTCATTCTCTCAACGCGAGTTTTCACTCACCCATCTTGTTCGTCTTCTGGTCTTTT[C/T]
TTTTGTTTCAGCGAGATCCCGTCGCGTCCCTCCCGCCATTCCAAGTCCGGCCAGTCTGAGGCCGAGGATCCGGCGACCGCAGAGGCCCGCAGGCGGCAAG
CTTGCCGCCTGCGGGCCTCTGCGGTCGCCGGATCCTCGGCCTCAGACTGGCCGGACTTGGAATGGCGGGAGGGACGCGACGGGATCTCGCTGAAACAAAA[G/A]
AAAAGACCAGAAGACGAACAAGATGGGTGAGTGAAAACTCGCGTTGAGAGAATGAATACAGCCACGATGGGTGAGAGACGAACCTGCGAGGGGGTCGGTT
| 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 | 8.10% | 0.10% | 5.52% | 86.29% | NA |
| All Indica | 2759 | 2.20% | 0.10% | 7.76% | 89.85% | NA |
| All Japonica | 1512 | 20.20% | 0.00% | 0.99% | 78.77% | NA |
| Aus | 269 | 1.10% | 0.40% | 6.69% | 91.82% | NA |
| Indica I | 595 | 1.70% | 0.00% | 4.37% | 93.95% | NA |
| Indica II | 465 | 0.90% | 0.00% | 7.53% | 91.61% | NA |
| Indica III | 913 | 4.10% | 0.30% | 10.08% | 85.54% | NA |
| Indica Intermediate | 786 | 1.40% | 0.10% | 7.76% | 90.71% | NA |
| Temperate Japonica | 767 | 34.40% | 0.00% | 0.00% | 65.58% | NA |
| Tropical Japonica | 504 | 3.80% | 0.00% | 2.38% | 93.85% | NA |
| Japonica Intermediate | 241 | 9.50% | 0.00% | 1.24% | 89.21% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 6.25% | 91.67% | NA |
| Intermediate | 90 | 10.00% | 0.00% | 8.89% | 81.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607893783 | C -> T | LOC_Os06g14140.1 | upstream_gene_variant ; 4045.0bp to feature; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893783 | C -> T | LOC_Os06g14160.1 | downstream_gene_variant ; 2696.0bp to feature; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893783 | C -> T | LOC_Os06g14150.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893783 | C -> DEL | N | N | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |