| Variant ID: vg0607893778 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7893778 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGTTTAACCGACCCCCTCGCAGGTTCGTCTCTCACCCATCGTGGCTGTATTCATTCTCTCAACGCGAGTTTTCACTCACCCATCTTGTTCGTCTTCTGGT[C/T]
TTTTCTTTTGTTTCAGCGAGATCCCGTCGCGTCCCTCCCGCCATTCCAAGTCCGGCCAGTCTGAGGCCGAGGATCCGGCGACCGCAGAGGCCCGCAGGCG
CGCCTGCGGGCCTCTGCGGTCGCCGGATCCTCGGCCTCAGACTGGCCGGACTTGGAATGGCGGGAGGGACGCGACGGGATCTCGCTGAAACAAAAGAAAA[G/A]
ACCAGAAGACGAACAAGATGGGTGAGTGAAAACTCGCGTTGAGAGAATGAATACAGCCACGATGGGTGAGAGACGAACCTGCGAGGGGGTCGGTTAAACG
| 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 | 7.80% | 0.10% | 1.35% | 90.73% | NA |
| All Indica | 2759 | 1.70% | 0.20% | 1.96% | 96.09% | NA |
| All Japonica | 1512 | 20.20% | 0.00% | 0.26% | 79.56% | NA |
| Aus | 269 | 1.10% | 0.00% | 1.49% | 97.40% | NA |
| Indica I | 595 | 1.50% | 0.00% | 1.18% | 97.31% | NA |
| Indica II | 465 | 0.90% | 0.00% | 1.29% | 97.85% | NA |
| Indica III | 913 | 2.80% | 0.70% | 2.96% | 93.54% | NA |
| Indica Intermediate | 786 | 1.10% | 0.00% | 1.78% | 97.07% | NA |
| Temperate Japonica | 767 | 34.30% | 0.00% | 0.13% | 65.58% | NA |
| Tropical Japonica | 504 | 3.80% | 0.00% | 0.40% | 95.83% | NA |
| Japonica Intermediate | 241 | 9.50% | 0.00% | 0.41% | 90.04% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 1.04% | 96.88% | NA |
| Intermediate | 90 | 11.10% | 0.00% | 1.11% | 87.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607893778 | C -> T | LOC_Os06g14140.1 | upstream_gene_variant ; 4040.0bp to feature; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893778 | C -> T | LOC_Os06g14160.1 | downstream_gene_variant ; 2701.0bp to feature; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893778 | C -> T | LOC_Os06g14150.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893778 | C -> DEL | N | N | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |