| Variant ID: vg0620602324 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20602324 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCCCTTCGCCAACCGTCATACCTACCGCTATATAAAGACATCACTCCCTCACTTCACTTACACACTTCCAAGCTTGAGCTGAATTATAAGAGGCTCTATT[G/A]
TACTATATTGTATACTAGAATAGGAAGAGAGTAGAGTAGAAGAAGTCGGAAGAATTCCGGAGTTGTCAGTAATCTTCTCCTATTTCTTTTATTCTGTTTA
TAAACAGAATAAAAGAAATAGGAGAAGATTACTGACAACTCCGGAATTCTTCCGACTTCTTCTACTCTACTCTCTTCCTATTCTAGTATACAATATAGTA[C/T]
AATAGAGCCTCTTATAATTCAGCTCAAGCTTGGAAGTGTGTAAGTGAAGTGAGGGAGTGATGTCTTTATATAGCGGTAGGTATGACGGTTGGCGAAGGGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.60% | 16.10% | 0.13% | 1.16% | NA |
| All Indica | 2759 | 98.90% | 1.10% | 0.00% | 0.07% | NA |
| All Japonica | 1512 | 49.30% | 46.90% | 0.40% | 3.37% | 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 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.20% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 98.00% | 1.90% | 0.00% | 0.13% | NA |
| Temperate Japonica | 767 | 79.80% | 19.00% | 0.39% | 0.78% | NA |
| Tropical Japonica | 504 | 10.90% | 87.90% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 32.80% | 49.80% | 1.24% | 16.18% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 74.40% | 23.30% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620602324 | G -> A | LOC_Os06g35340.1 | intron_variant ; MODIFIER | silent_mutation | Average:8.197; most accessible tissue: Minghui63 root, score: 10.708 | N | N | N | N |
| vg0620602324 | G -> DEL | N | N | silent_mutation | Average:8.197; most accessible tissue: Minghui63 root, score: 10.708 | N | N | N | N |