| Variant ID: vg0318608317 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18608317 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACGCAAGGGAGAGAAAAACAACACACACACACACACACACACTGTTAAATAAACCGACAGCAAATTGGGGGGGCAACACGAAATCGGGCGCGCCACCCAC[C/A]
CACCCACCTTCCTCCTCGTCGCTGCGCCCCTGGACGATCTGCGCCTTCACCTCCTCGAACAGCAGCGGCTCGAACACAGCGAGGTACTCGGCCACCGAGG
CCTCGGTGGCCGAGTACCTCGCTGTGTTCGAGCCGCTGCTGTTCGAGGAGGTGAAGGCGCAGATCGTCCAGGGGCGCAGCGACGAGGAGGAAGGTGGGTG[G/T]
GTGGGTGGCGCGCCCGATTTCGTGTTGCCCCCCCAATTTGCTGTCGGTTTATTTAACAGTGTGTGTGTGTGTGTGTGTGTTGTTTTTCTCTCCCTTGCGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.10% | 1.00% | 2.45% | 0.53% | NA |
| All Indica | 2759 | 95.70% | 1.60% | 2.61% | 0.14% | NA |
| All Japonica | 1512 | 95.90% | 0.00% | 2.78% | 1.32% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.00% | 0.50% | 0.00% | NA |
| Indica II | 465 | 96.30% | 0.20% | 2.80% | 0.65% | NA |
| Indica III | 913 | 91.70% | 3.70% | 4.60% | 0.00% | NA |
| Indica Intermediate | 786 | 96.90% | 1.10% | 1.78% | 0.13% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 88.90% | 0.00% | 7.14% | 3.97% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 2.49% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 1.10% | 2.22% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318608317 | C -> A | LOC_Os03g32526.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:22.4; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0318608317 | C -> A | LOC_Os03g32540.1 | upstream_gene_variant ; 2876.0bp to feature; MODIFIER | silent_mutation | Average:22.4; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0318608317 | C -> DEL | N | N | silent_mutation | Average:22.4; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |