| Variant ID: vg0604193650 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 4193650 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GGGAAGAGAGTGGCAGGCAAGCATGCATACACGTTCGGCGATGCTGTGTGGGTCGGTGGCTTGCCCTCTCCTCGCGCGCACCCGCTGCTGCCGCGGCGGC[G/C]
CCGTGCCACCGCCACCGGAGGAGGTGACCGGCGCCGTGCCTCCGCTCGCCGCCGGCCCTCCGAAGCTCTGCCCCGACATTGATCCTCCCTTGAAACGACG
CGTCGTTTCAAGGGAGGATCAATGTCGGGGCAGAGCTTCGGAGGGCCGGCGGCGAGCGGAGGCACGGCGCCGGTCACCTCCTCCGGTGGCGGTGGCACGG[C/G]
GCCGCCGCGGCAGCAGCGGGTGCGCGCGAGGAGAGGGCAAGCCACCGACCCACACAGCATCGCCGAACGTGTATGCATGCTTGCCTGCCACTCTCTTCCC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.90% | 0.10% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.10% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.40% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0604193650 | G -> C | LOC_Os06g08490.1 | upstream_gene_variant ; 3087.0bp to feature; MODIFIER | N | Average:64.776; most accessible tissue: Minghui63 panicle, score: 82.128 | N | N | N | N |
| vg0604193650 | G -> C | LOC_Os06g08500.1 | intron_variant ; MODIFIER | N | Average:64.776; most accessible tissue: Minghui63 panicle, score: 82.128 | N | N | N | N |