| Variant ID: vg0607893756 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7893756 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTCATTTCCCCTCCAAAGTGGTCGTTTAACCGACCCCCTCGCAGGTTCGTCTCTCACCCATCGTGGCTGTATTCATTCTCTCAACGCGAGTTTTCACTCA[C/T]
CCATCTTGTTCGTCTTCTGGTCTTTTCTTTTGTTTCAGCGAGATCCCGTCGCGTCCCTCCCGCCATTCCAAGTCCGGCCAGTCTGAGGCCGAGGATCCGG
CCGGATCCTCGGCCTCAGACTGGCCGGACTTGGAATGGCGGGAGGGACGCGACGGGATCTCGCTGAAACAAAAGAAAAGACCAGAAGACGAACAAGATGG[G/A]
TGAGTGAAAACTCGCGTTGAGAGAATGAATACAGCCACGATGGGTGAGAGACGAACCTGCGAGGGGGTCGGTTAAACGACCACTTTGGAGGGGAAATGAG
| 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 | 7.00% | 0.40% | 1.69% | 90.88% | NA |
| All Indica | 2759 | 0.80% | 0.70% | 2.07% | 96.48% | NA |
| All Japonica | 1512 | 19.80% | 0.00% | 0.26% | 79.89% | NA |
| Aus | 269 | 0.40% | 0.00% | 5.95% | 93.68% | NA |
| Indica I | 595 | 1.00% | 0.30% | 1.01% | 97.65% | NA |
| Indica II | 465 | 0.40% | 0.40% | 0.43% | 98.71% | NA |
| Indica III | 913 | 1.30% | 1.50% | 3.61% | 93.54% | NA |
| Indica Intermediate | 786 | 0.30% | 0.00% | 2.04% | 97.71% | NA |
| Temperate Japonica | 767 | 34.30% | 0.00% | 0.13% | 65.58% | NA |
| Tropical Japonica | 504 | 3.40% | 0.00% | 0.60% | 96.03% | NA |
| Japonica Intermediate | 241 | 8.30% | 0.00% | 0.00% | 91.70% | NA |
| VI/Aromatic | 96 | 0.00% | 1.00% | 3.12% | 95.83% | NA |
| Intermediate | 90 | 10.00% | 0.00% | 0.00% | 90.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607893756 | C -> T | LOC_Os06g14140.1 | upstream_gene_variant ; 4018.0bp to feature; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893756 | C -> T | LOC_Os06g14160.1 | downstream_gene_variant ; 2723.0bp to feature; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893756 | C -> T | LOC_Os06g14150.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893756 | C -> DEL | N | N | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |