| Variant ID: vg0322194333 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22194333 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCCGAAGCATGCCGGGCCCTACCTCACTCGCCAAGCGGAGGGCCTCGACCTCCCCGGCGGACGAGTCCAGCGCGCCCTGCAGCTTGGCGATGGTGTGTTC[G/A]
GCGGCTGCGAGGCGGGCGGCTAGGTCGCCGTGGCCCGCGGCCGCCCCGCCGCTGTGCGCTCTCGCGTCCAGCTCCTTCGCCCGCGCCTCGAGCTCAGCGG
CCGCTGAGCTCGAGGCGCGGGCGAAGGAGCTGGACGCGAGAGCGCACAGCGGCGGGGCGGCCGCGGGCCACGGCGACCTAGCCGCCCGCCTCGCAGCCGC[C/T]
GAACACACCATCGCCAAGCTGCAGGGCGCGCTGGACTCGTCCGCCGGGGAGGTCGAGGCCCTCCGCTTGGCGAGTGAGGTAGGGCCCGGCATGCTTCGGG
| 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 | 7.20% | 2.50% | 17.96% | 72.39% | NA |
| All Indica | 2759 | 0.40% | 0.00% | 24.68% | 74.95% | NA |
| All Japonica | 1512 | 21.10% | 7.50% | 4.23% | 67.13% | NA |
| Aus | 269 | 0.40% | 0.00% | 35.69% | 63.94% | NA |
| Indica I | 595 | 0.00% | 0.00% | 16.81% | 83.19% | NA |
| Indica II | 465 | 0.60% | 0.00% | 5.81% | 93.55% | NA |
| Indica III | 913 | 0.00% | 0.00% | 44.69% | 55.31% | NA |
| Indica Intermediate | 786 | 0.90% | 0.00% | 18.58% | 80.53% | NA |
| Temperate Japonica | 767 | 15.40% | 0.00% | 3.00% | 81.62% | NA |
| Tropical Japonica | 504 | 30.80% | 20.20% | 5.16% | 43.85% | NA |
| Japonica Intermediate | 241 | 19.10% | 5.00% | 6.22% | 69.71% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 1.04% | 97.92% | NA |
| Intermediate | 90 | 10.00% | 2.20% | 7.78% | 80.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322194333 | G -> A | LOC_Os03g39930.1 | synonymous_variant ; p.Ala263Ala; LOW | synonymous_codon | Average:7.955; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg0322194333 | G -> DEL | LOC_Os03g39930.1 | N | frameshift_variant | Average:7.955; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |