| Variant ID: vg0607893742 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7893742 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CATCTCGGGGAAAGCTCATTTCCCCTCCAAAGTGGTCGTTTAACCGACCCCCTCGCAGGTTCGTCTCTCACCCATCGTGGCTGTATTCATTCTCTCAACG[C/T]
GAGTTTTCACTCACCCATCTTGTTCGTCTTCTGGTCTTTTCTTTTGTTTCAGCGAGATCCCGTCGCGTCCCTCCCGCCATTCCAAGTCCGGCCAGTCTGA
TCAGACTGGCCGGACTTGGAATGGCGGGAGGGACGCGACGGGATCTCGCTGAAACAAAAGAAAAGACCAGAAGACGAACAAGATGGGTGAGTGAAAACTC[G/A]
CGTTGAGAGAATGAATACAGCCACGATGGGTGAGAGACGAACCTGCGAGGGGGTCGGTTAAACGACCACTTTGGAGGGGAAATGAGCTTTCCCCGAGATG
| 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 | 16.30% | 0.10% | 14.16% | 69.40% | NA |
| All Indica | 2759 | 14.80% | 0.20% | 21.42% | 63.65% | NA |
| All Japonica | 1512 | 20.00% | 0.00% | 1.12% | 78.84% | NA |
| Aus | 269 | 13.40% | 0.00% | 12.64% | 73.98% | NA |
| Indica I | 595 | 7.40% | 0.20% | 16.47% | 75.97% | NA |
| Indica II | 465 | 9.70% | 0.20% | 11.61% | 78.49% | NA |
| Indica III | 913 | 24.00% | 0.20% | 29.03% | 46.77% | NA |
| Indica Intermediate | 786 | 12.60% | 0.10% | 22.14% | 65.14% | NA |
| Temperate Japonica | 767 | 34.40% | 0.00% | 0.26% | 65.32% | NA |
| Tropical Japonica | 504 | 3.40% | 0.00% | 1.98% | 94.64% | NA |
| Japonica Intermediate | 241 | 9.10% | 0.00% | 2.07% | 88.80% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 17.71% | 75.00% | NA |
| Intermediate | 90 | 21.10% | 0.00% | 11.11% | 67.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607893742 | C -> T | LOC_Os06g14140.1 | upstream_gene_variant ; 4004.0bp to feature; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893742 | C -> T | LOC_Os06g14160.1 | downstream_gene_variant ; 2737.0bp to feature; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893742 | C -> T | LOC_Os06g14150.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893742 | C -> DEL | N | N | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |