| Variant ID: vg0318608640 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18608640 |
| Reference Allele: C | Alternative Allele: G,T |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGGGGCGGGGAGGGGCGTACCTTGGAGTCCGCGACGAGGCGGACGTAGTCCCAGCTGAGGACGATCTTGTGGAAGCGGTCCATGGTGGAGGCGGCGACGC[C/G,T]
CGACGAGGAGGAGGAGGCGCCGCCTCCGCCTCCGCCGCCGCCGGATTTGTCCACCGCCATTGGGGCGGCGGCGCGGCGGCGCGGCGGCGAGAGAAGGGGG
CCCCCTTCTCTCGCCGCCGCGCCGCCGCGCCGCCGCCCCAATGGCGGTGGACAAATCCGGCGGCGGCGGAGGCGGAGGCGGCGCCTCCTCCTCCTCGTCG[G/C,A]
GCGTCGCCGCCTCCACCATGGACCGCTTCCACAAGATCGTCCTCAGCTGGGACTACGTCCGCCTCGTCGCGGACTCCAAGGTACGCCCCTCCCCGCCCCG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.30% | 0.00% | 0.23% | 0.38% | T: 0.02% |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 98.10% | 0.00% | 0.73% | 1.12% | T: 0.07% |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 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 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 94.40% | 0.00% | 2.18% | 3.37% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.00% | T: 0.41% |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318608640 | C -> T | LOC_Os03g32526.1 | missense_variant ; p.Gly21Ser; MODERATE | nonsynonymous_codon ; G21S | Average:32.006; most accessible tissue: Minghui63 young leaf, score: 63.571 | unknown | unknown | TOLERATED | 0.69 |
| vg0318608640 | C -> DEL | LOC_Os03g32526.1 | N | frameshift_variant | Average:32.006; most accessible tissue: Minghui63 young leaf, score: 63.571 | N | N | N | N |
| vg0318608640 | C -> G | LOC_Os03g32526.1 | missense_variant ; p.Gly21Arg; MODERATE | nonsynonymous_codon ; G21R | Average:32.006; most accessible tissue: Minghui63 young leaf, score: 63.571 | unknown | unknown | DELETERIOUS | 0.02 |