| Variant ID: vg0410079375 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10079375 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAGAACAAGCAGACGGACGGTCTAGCCGACACGCGCGCTGCAAGCAAGTAGCAATGGCTAAACTTTAATCTATCAAAACCCAAGAAACCCTGAAGGGGTA[C/A]
CTAACTATATAAATAGGGGTGGGAGGACGACCTAGGGGTGCCTAGGGTCGTGCTCCACCTGGCTGGGGCGCACCCCACATGGGCCCCACCTGGGCCGGGG
CCCCGGCCCAGGTGGGGCCCATGTGGGGTGCGCCCCAGCCAGGTGGAGCACGACCCTAGGCACCCCTAGGTCGTCCTCCCACCCCTATTTATATAGTTAG[G/T]
TACCCCTTCAGGGTTTCTTGGGTTTTGATAGATTAAAGTTTAGCCATTGCTACTTGCTTGCAGCGCGCGTGTCGGCTAGACCGTCCGTCTGCTTGTTCTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 31.30% | 0.70% | 13.88% | 54.19% | NA |
| All Indica | 2759 | 7.10% | 1.10% | 18.19% | 73.54% | NA |
| All Japonica | 1512 | 77.70% | 0.00% | 6.88% | 15.41% | NA |
| Aus | 269 | 5.60% | 0.00% | 8.55% | 85.87% | NA |
| Indica I | 595 | 4.50% | 1.70% | 18.32% | 75.46% | NA |
| Indica II | 465 | 7.30% | 1.30% | 16.56% | 74.84% | NA |
| Indica III | 913 | 8.50% | 0.10% | 21.80% | 69.55% | NA |
| Indica Intermediate | 786 | 7.40% | 1.80% | 14.89% | 75.95% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.65% | 2.87% | NA |
| Tropical Japonica | 504 | 50.80% | 0.00% | 18.25% | 30.95% | NA |
| Japonica Intermediate | 241 | 74.30% | 0.00% | 2.90% | 22.82% | NA |
| VI/Aromatic | 96 | 51.00% | 0.00% | 17.71% | 31.25% | NA |
| Intermediate | 90 | 46.70% | 0.00% | 11.11% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410079375 | C -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0410079375 | C -> A | LOC_Os04g18230.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |