| Variant ID: vg0415576085 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15576085 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCATCTTTTTTTTTTTTACAATTTGTGATTCACTAAGATGTATAATTTTGTGATTTGTTGCATGATCTGAGATGTATAATCTATGATGTATTTGGTTTGT[G/A]
TGTAATTTTTTTAAGATTTGTGATGTATTTGATTTGTGTGTATAAGTAACTTAAGATTTGTGATGTGAATGTTTTGGGATGTTACTTTGATTTGAGGTGA
TCACCTCAAATCAAAGTAACATCCCAAAACATTCACATCACAAATCTTAAGTTACTTATACACACAAATCAAATACATCACAAATCTTAAAAAAATTACA[C/T]
ACAAACCAAATACATCATAGATTATACATCTCAGATCATGCAACAAATCACAAAATTATACATCTTAGTGAATCACAAATTGTAAAAAAAAAAAAGATGC
| 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 | 63.20% | 0.20% | 13.20% | 23.38% | NA |
| All Indica | 2759 | 67.30% | 0.30% | 14.72% | 17.72% | NA |
| All Japonica | 1512 | 67.00% | 0.00% | 10.98% | 22.02% | NA |
| Aus | 269 | 3.70% | 0.00% | 0.74% | 95.54% | NA |
| Indica I | 595 | 86.40% | 0.00% | 2.35% | 11.26% | NA |
| Indica II | 465 | 60.00% | 0.00% | 10.32% | 29.68% | NA |
| Indica III | 913 | 57.50% | 0.80% | 24.75% | 16.98% | NA |
| Indica Intermediate | 786 | 68.40% | 0.10% | 15.01% | 16.41% | NA |
| Temperate Japonica | 767 | 44.50% | 0.00% | 14.73% | 40.81% | NA |
| Tropical Japonica | 504 | 91.50% | 0.00% | 7.34% | 1.19% | NA |
| Japonica Intermediate | 241 | 87.60% | 0.00% | 6.64% | 5.81% | NA |
| VI/Aromatic | 96 | 52.10% | 0.00% | 38.54% | 9.38% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 14.44% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415576085 | G -> DEL | N | N | silent_mutation | Average:20.424; most accessible tissue: Zhenshan97 flag leaf, score: 30.355 | N | N | N | N |
| vg0415576085 | G -> A | LOC_Os04g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:20.424; most accessible tissue: Zhenshan97 flag leaf, score: 30.355 | N | N | N | N |