| Variant ID: vg0318608678 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18608678 |
| Reference Allele: C | Alternative Allele: T,G |
| Primary Allele: C | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
GCGGACGTAGTCCCAGCTGAGGACGATCTTGTGGAAGCGGTCCATGGTGGAGGCGGCGACGCCCGACGAGGAGGAGGAGGCGCCGCCTCCGCCTCCGCCG[C/T,G]
CGCCGGATTTGTCCACCGCCATTGGGGCGGCGGCGCGGCGGCGCGGCGGCGAGAGAAGGGGGTTCTGGGGTTTAGTGAGCCGCCGGCGCTGCAGCGGCAA
TTGCCGCTGCAGCGCCGGCGGCTCACTAAACCCCAGAACCCCCTTCTCTCGCCGCCGCGCCGCCGCGCCGCCGCCCCAATGGCGGTGGACAAATCCGGCG[G/A,C]
CGGCGGAGGCGGAGGCGGCGCCTCCTCCTCCTCGTCGGGCGTCGCCGCCTCCACCATGGACCGCTTCCACAAGATCGTCCTCAGCTGGGACTACGTCCGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.40% | 0.00% | 0.38% | 0.21% | NA |
| All Indica | 2759 | 99.50% | 0.00% | 0.18% | 0.36% | NA |
| All Japonica | 1512 | 99.20% | 0.00% | 0.79% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 98.10% | 0.00% | 0.22% | 1.72% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.00% | 0.38% | 0.25% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.60% | 0.00% | 2.38% | 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% | 0.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318608678 | C -> T | LOC_Os03g32526.1 | missense_variant ; p.Gly8Asp; MODERATE | N | Average:32.741; most accessible tissue: Minghui63 young leaf, score: 65.92 | N | N | N | N |
| vg0318608678 | C -> T | LOC_Os03g32540.1 | upstream_gene_variant ; 2515.0bp to feature; MODIFIER | N | Average:32.741; most accessible tissue: Minghui63 young leaf, score: 65.92 | N | N | N | N |
| vg0318608678 | C -> G | LOC_Os03g32526.1 | missense_variant ; p.Gly8Ala; MODERATE | N | Average:32.741; most accessible tissue: Minghui63 young leaf, score: 65.92 | N | N | N | N |
| vg0318608678 | C -> G | LOC_Os03g32540.1 | upstream_gene_variant ; 2515.0bp to feature; MODIFIER | N | Average:32.741; most accessible tissue: Minghui63 young leaf, score: 65.92 | N | N | N | N |