| Variant ID: vg0322194102 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22194102 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGTCAGGGTCCCTGGCCTGGTAGCTTGCCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGG[G/A]
AGCCGCTGGAGGGCCCCGGCCATCTCTGAGAGGCACTGGGCGAGGCCCCCCTGGTTGGCGGCGTACTTCGCGTGCCGCCCGCCCCAGAGACCCGCCTGCC
GGCAGGCGGGTCTCTGGGGCGGGCGGCACGCGAAGTACGCCGCCAACCAGGGGGGCCTCGCCCAGTGCCTCTCAGAGATGGCCGGGGCCCTCCAGCGGCT[C/T]
CCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGGCAAGCTACCAGGCCAGGGACCCTGACT
| 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 | 31.20% | 0.20% | 5.61% | 62.97% | NA |
| All Indica | 2759 | 31.80% | 0.30% | 7.58% | 60.35% | NA |
| All Japonica | 1512 | 31.00% | 0.00% | 1.65% | 67.33% | NA |
| Aus | 269 | 39.00% | 0.00% | 3.35% | 57.62% | NA |
| Indica I | 595 | 16.80% | 0.50% | 2.02% | 80.67% | NA |
| Indica II | 465 | 14.00% | 0.00% | 13.12% | 72.90% | NA |
| Indica III | 913 | 56.10% | 0.20% | 9.09% | 34.61% | NA |
| Indica Intermediate | 786 | 25.30% | 0.50% | 6.74% | 67.43% | NA |
| Temperate Japonica | 767 | 15.50% | 0.00% | 0.78% | 83.70% | NA |
| Tropical Japonica | 504 | 56.20% | 0.00% | 1.98% | 41.87% | NA |
| Japonica Intermediate | 241 | 27.80% | 0.00% | 3.73% | 68.46% | NA |
| VI/Aromatic | 96 | 6.20% | 0.00% | 16.67% | 77.08% | NA |
| Intermediate | 90 | 22.20% | 0.00% | 6.67% | 71.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322194102 | G -> A | LOC_Os03g39930.1 | synonymous_variant ; p.Leu340Leu; LOW | synonymous_codon | Average:6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |
| vg0322194102 | G -> DEL | LOC_Os03g39930.1 | N | frameshift_variant | Average:6.269; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |