| Variant ID: vg0620602381 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20602381 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTACACACTTCCAAGCTTGAGCTGAATTATAAGAGGCTCTATTGTACTATATTGTATACTAGAATAGGAAGAGAGTAGAGTAGAAGAAGTCGGAAGAATT[C/T]
CGGAGTTGTCAGTAATCTTCTCCTATTTCTTTTATTCTGTTTATTACTCTGAATTCAATATAATATTATTCCTAAGTAATTTAGATTTATCTTGTGAGAA
TTCTCACAAGATAAATCTAAATTACTTAGGAATAATATTATATTGAATTCAGAGTAATAAACAGAATAAAAGAAATAGGAGAAGATTACTGACAACTCCG[G/A]
AATTCTTCCGACTTCTTCTACTCTACTCTCTTCCTATTCTAGTATACAATATAGTACAATAGAGCCTCTTATAATTCAGCTCAAGCTTGGAAGTGTGTAA
| 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 | 98.60% | 0.20% | 0.00% | 1.18% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
| All Japonica | 1512 | 96.00% | 0.60% | 0.00% | 3.44% | 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 | 99.90% | 0.00% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 97.20% | 1.80% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 83.00% | 0.00% | 0.00% | 17.01% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0620602381 | C -> T | LOC_Os06g35340.1 | intron_variant ; MODIFIER | silent_mutation | Average:8.32; most accessible tissue: Minghui63 flower, score: 11.139 | N | N | N | N |
| vg0620602381 | C -> DEL | N | N | silent_mutation | Average:8.32; most accessible tissue: Minghui63 flower, score: 11.139 | N | N | N | N |