| Variant ID: vg0300825951 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 825951 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CCCCGACGACCGGAGTTGACCCTCTGCGCGCTTGTCAGACGGTGCTAGGAGCCCCCGACCCCCAGGAAGGCCCTGAGGCCACTGTGGGAAGGCCGCACCT[A/G]
TCGCCCTTTGACCCCGAGGCTAACCCTGTGCTGACTCGACCCGGGAAAGAGCAGGGAGAAGAGGCCCCCGAGCCGAACGGAGGCCTAAGGCCCCTGACGA
TCGTCAGGGGCCTTAGGCCTCCGTTCGGCTCGGGGGCCTCTTCTCCCTGCTCTTTCCCGGGTCGAGTCAGCACAGGGTTAGCCTCGGGGTCAAAGGGCGA[T/C]
AGGTGCGGCCTTCCCACAGTGGCCTCAGGGCCTTCCTGGGGGTCGGGGGCTCCTAGCACCGTCTGACAAGCGCGCAGAGGGTCAACTCCGGTCGTCGGGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 15.40% | 0.50% | 3.00% | 81.08% | NA |
| All Indica | 2759 | 4.30% | 0.80% | 3.88% | 91.08% | NA |
| All Japonica | 1512 | 37.80% | 0.00% | 0.79% | 61.44% | NA |
| Aus | 269 | 1.50% | 0.40% | 0.74% | 97.40% | NA |
| Indica I | 595 | 6.20% | 0.00% | 3.19% | 90.59% | NA |
| Indica II | 465 | 8.20% | 0.20% | 3.01% | 88.60% | NA |
| Indica III | 913 | 1.20% | 1.50% | 4.60% | 92.66% | NA |
| Indica Intermediate | 786 | 4.10% | 0.80% | 4.07% | 91.09% | NA |
| Temperate Japonica | 767 | 61.30% | 0.00% | 0.65% | 38.07% | NA |
| Tropical Japonica | 504 | 6.90% | 0.00% | 0.60% | 92.46% | NA |
| Japonica Intermediate | 241 | 27.40% | 0.00% | 1.66% | 70.95% | NA |
| VI/Aromatic | 96 | 20.80% | 1.00% | 18.75% | 59.38% | NA |
| Intermediate | 90 | 17.80% | 0.00% | 3.33% | 78.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0300825951 | A -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0300825951 | A -> G | LOC_Os03g02350.1 | synonymous_variant ; p.Leu1210Leu; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |