| Variant ID: vg0322194129 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22194129 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGGGAGCCGCTGGAGGGCCCCGGCCATCTC[T/C]
GAGAGGCACTGGGCGAGGCCCCCCTGGTTGGCGGCGTACTTCGCGTGCCGCCCGCCCCAGAGACCCGCCTGCCGCCCGGCGCGGTCTAGACGGGAGACGG
CCGTCTCCCGTCTAGACCGCGCCGGGCGGCAGGCGGGTCTCTGGGGCGGGCGGCACGCGAAGTACGCCGCCAACCAGGGGGGCCTCGCCCAGTGCCTCTC[A/G]
GAGATGGCCGGGGCCCTCCAGCGGCTCCCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 8.50% | 0.10% | 3.77% | 87.60% | NA |
| All Indica | 2759 | 0.70% | 0.10% | 2.65% | 96.59% | NA |
| All Japonica | 1512 | 25.00% | 0.10% | 6.35% | 68.58% | NA |
| Aus | 269 | 0.00% | 0.40% | 0.74% | 98.88% | NA |
| Indica I | 595 | 0.20% | 0.00% | 0.34% | 99.50% | NA |
| Indica II | 465 | 0.20% | 0.00% | 0.22% | 99.57% | NA |
| Indica III | 913 | 0.50% | 0.30% | 6.57% | 92.55% | NA |
| Indica Intermediate | 786 | 1.40% | 0.00% | 1.27% | 97.33% | NA |
| Temperate Japonica | 767 | 9.30% | 0.00% | 5.48% | 85.27% | NA |
| Tropical Japonica | 504 | 51.40% | 0.20% | 6.55% | 41.87% | NA |
| Japonica Intermediate | 241 | 19.90% | 0.00% | 8.71% | 71.37% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 1.04% | 98.96% | NA |
| Intermediate | 90 | 7.80% | 0.00% | 6.67% | 85.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322194129 | T -> C | LOC_Os03g39930.1 | synonymous_variant ; p.Ser331Ser; LOW | synonymous_codon | Average:6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |
| vg0322194129 | T -> DEL | LOC_Os03g39930.1 | N | frameshift_variant | Average:6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |