| Variant ID: vg0322194078 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22194078 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTTCCAGCGCTGCCCACGGGGAGAAGTCAGGGTCCCTGGCCTGGTAGCTTGCCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTT[G/A]
ATCGTCTCCTCGAGCTCCTCGGGGAGCCGCTGGAGGGCCCCGGCCATCTCTGAGAGGCACTGGGCGAGGCCCCCCTGGTTGGCGGCGTACTTCGCGTGCC
GGCACGCGAAGTACGCCGCCAACCAGGGGGGCCTCGCCCAGTGCCTCTCAGAGATGGCCGGGGCCCTCCAGCGGCTCCCCGAGGAGCTCGAGGAGACGAT[C/T]
AAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGGCAAGCTACCAGGCCAGGGACCCTGACTTCTCCCCGTGGGCAGCGCTGGAAG
| 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 | 39.70% | 0.10% | 0.93% | 59.20% | NA |
| All Indica | 2759 | 43.60% | 0.30% | 0.98% | 55.20% | NA |
| All Japonica | 1512 | 32.60% | 0.00% | 0.93% | 66.47% | NA |
| Aus | 269 | 46.10% | 0.00% | 0.74% | 53.16% | NA |
| Indica I | 595 | 22.00% | 0.00% | 0.84% | 77.14% | NA |
| Indica II | 465 | 28.40% | 0.60% | 2.37% | 68.60% | NA |
| Indica III | 913 | 70.80% | 0.10% | 0.44% | 28.70% | NA |
| Indica Intermediate | 786 | 37.30% | 0.40% | 0.89% | 61.45% | NA |
| Temperate Japonica | 767 | 15.50% | 0.00% | 0.78% | 83.70% | NA |
| Tropical Japonica | 504 | 58.50% | 0.00% | 0.99% | 40.48% | NA |
| Japonica Intermediate | 241 | 32.80% | 0.00% | 1.24% | 65.98% | NA |
| VI/Aromatic | 96 | 27.10% | 0.00% | 1.04% | 71.88% | NA |
| Intermediate | 90 | 35.60% | 0.00% | 0.00% | 64.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322194078 | G -> A | LOC_Os03g39930.1 | synonymous_variant ; p.Ile348Ile; LOW | synonymous_codon | Average:6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |
| vg0322194078 | G -> DEL | LOC_Os03g39930.1 | N | frameshift_variant | Average:6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |