| Variant ID: vg0318608620 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18608620 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGCAAAGCGAGCGCTCGGGGCGGGGCGGGGAGGGGCGTACCTTGGAGTCCGCGACGAGGCGGACGTAGTCCCAGCTGAGGACGATCTTGTGGAAGCGGTC[C/T]
ATGGTGGAGGCGGCGACGCCCGACGAGGAGGAGGAGGCGCCGCCTCCGCCTCCGCCGCCGCCGGATTTGTCCACCGCCATTGGGGCGGCGGCGCGGCGGC
GCCGCCGCGCCGCCGCCCCAATGGCGGTGGACAAATCCGGCGGCGGCGGAGGCGGAGGCGGCGCCTCCTCCTCCTCGTCGGGCGTCGCCGCCTCCACCAT[G/A]
GACCGCTTCCACAAGATCGTCCTCAGCTGGGACTACGTCCGCCTCGTCGCGGACTCCAAGGTACGCCCCTCCCCGCCCCGCCCCGAGCGCTCGCTTTGCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.30% | 0.10% | 0.19% | 0.38% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 98.30% | 0.00% | 0.60% | 1.12% | NA |
| Aus | 269 | 99.30% | 0.70% | 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 | 94.80% | 0.00% | 1.79% | 3.37% | 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% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0318608620 | C -> T | LOC_Os03g32526.1 | missense_variant ; p.Met27Ile; MODERATE | nonsynonymous_codon ; M27I | Average:31.851; most accessible tissue: Minghui63 young leaf, score: 63.571 | unknown | unknown | TOLERATED | 0.76 |
| vg0318608620 | C -> DEL | LOC_Os03g32526.1 | N | frameshift_variant | Average:31.851; most accessible tissue: Minghui63 young leaf, score: 63.571 | N | N | N | N |