| Variant ID: vg0605309582 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 5309582 |
| Reference Allele: AG | Alternative Allele: A |
| Primary Allele: AG | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGAGACAGGATTTTGAAAAAGGGGGGGGGGGGGAAGGTGATTGATTGGCTCGTTGAATTTTTGATGATTTTTATAATGTCTATTTCATAGTATTAATAGT[AG/A]
TATGCACAAGAAATAAACGTGCTGATTCAGTCAAAGATTTTTTTAGAAAATAGTATACCTGGAGTAACTTCACGATGTCGCCTCATGATATATTGGATCT
AGATCCAATATATCATGAGGCGACATCGTGAAGTTACTCCAGGTATACTATTTTCTAAAAAAATCTTTGACTGAATCAGCACGTTTATTTCTTGTGCATA[CT/T]
ACTATTAATACTATGAAATAGACATTATAAAAATCATCAAAAATTCAACGAGCCAATCAATCACCTTCCCCCCCCCCCCCTTTTTCAAAATCCTGTCTCC
| Populations | Population Size | Frequency of AG(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.10% | 1.90% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 89.20% | 10.00% | 0.74% | 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 | 95.40% | 4.60% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.70% | 2.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 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 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0605309582 | AG -> A | LOC_Os06g10320.1 | downstream_gene_variant ; 2852.0bp to feature; MODIFIER | silent_mutation | Average:68.737; most accessible tissue: Minghui63 young leaf, score: 82.368 | N | N | N | N |
| vg0605309582 | AG -> A | LOC_Os06g10330.1 | downstream_gene_variant ; 1836.0bp to feature; MODIFIER | silent_mutation | Average:68.737; most accessible tissue: Minghui63 young leaf, score: 82.368 | N | N | N | N |
| vg0605309582 | AG -> A | LOC_Os06g10340.1 | intron_variant ; MODIFIER | silent_mutation | Average:68.737; most accessible tissue: Minghui63 young leaf, score: 82.368 | N | N | N | N |