| Variant ID: vg0410079383 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10079383 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCAGACGGACGGTCTAGCCGACACGCGCGCTGCAAGCAAGTAGCAATGGCTAAACTTTAATCTATCAAAACCCAAGAAACCCTGAAGGGGTACCTAACTA[T/A]
ATAAATAGGGGTGGGAGGACGACCTAGGGGTGCCTAGGGTCGTGCTCCACCTGGCTGGGGCGCACCCCACATGGGCCCCACCTGGGCCGGGGTCCCAGAC
GTCTGGGACCCCGGCCCAGGTGGGGCCCATGTGGGGTGCGCCCCAGCCAGGTGGAGCACGACCCTAGGCACCCCTAGGTCGTCCTCCCACCCCTATTTAT[A/T]
TAGTTAGGTACCCCTTCAGGGTTTCTTGGGTTTTGATAGATTAAAGTTTAGCCATTGCTACTTGCTTGCAGCGCGCGTGTCGGCTAGACCGTCCGTCTGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 28.00% | 0.40% | 5.08% | 66.48% | NA |
| All Indica | 2759 | 2.20% | 0.70% | 3.73% | 93.40% | NA |
| All Japonica | 1512 | 77.40% | 0.00% | 6.61% | 16.01% | NA |
| Aus | 269 | 1.50% | 0.40% | 6.32% | 91.82% | NA |
| Indica I | 595 | 2.20% | 0.50% | 3.36% | 93.95% | NA |
| Indica II | 465 | 2.40% | 0.40% | 3.23% | 93.98% | NA |
| Indica III | 913 | 1.50% | 1.10% | 4.16% | 93.21% | NA |
| Indica Intermediate | 786 | 2.80% | 0.50% | 3.82% | 92.88% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.52% | 3.00% | NA |
| Tropical Japonica | 504 | 50.00% | 0.00% | 17.86% | 32.14% | NA |
| Japonica Intermediate | 241 | 73.90% | 0.00% | 2.49% | 23.65% | NA |
| VI/Aromatic | 96 | 51.00% | 0.00% | 15.62% | 33.33% | NA |
| Intermediate | 90 | 45.60% | 0.00% | 5.56% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410079383 | T -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0410079383 | T -> A | LOC_Os04g18230.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |