| Variant ID: vg0721993438 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 21993438 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTACTATACATATACATTGGTGGAATGGGCCCTATTGGGCTGAAATACACACGCCTACACTCAACACTCCCCCTCAAGATGGGCGATAAATATCTATCAT[G/A]
CCCATCTTGCTACACGAAGAAGTGCACTCTCTAGCACCTAATGCCTTCGTTAAACTATCAGCTACTTGTTCACCAGAGTTTACAAAGCCTAAGTTTAAGG
CCTTAAACTTAGGCTTTGTAAACTCTGGTGAACAAGTAGCTGATAGTTTAACGAAGGCATTAGGTGCTAGAGAGTGCACTTCTTCGTGTAGCAAGATGGG[C/T]
ATGATAGATATTTATCGCCCATCTTGAGGGGGAGTGTTGAGTGTAGGCGTGTGTATTTCAGCCCAATAGGGCCCATTCCACCAATGTATATGTATAGTAG
| 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 | 92.50% | 1.60% | 3.45% | 2.39% | NA |
| All Indica | 2759 | 95.70% | 1.90% | 2.36% | 0.04% | NA |
| All Japonica | 1512 | 87.00% | 1.30% | 4.30% | 7.41% | NA |
| Aus | 269 | 87.70% | 1.10% | 11.15% | 0.00% | NA |
| Indica I | 595 | 97.30% | 0.80% | 1.85% | 0.00% | NA |
| Indica II | 465 | 94.40% | 1.90% | 3.44% | 0.22% | NA |
| Indica III | 913 | 96.30% | 2.30% | 1.42% | 0.00% | NA |
| Indica Intermediate | 786 | 94.70% | 2.20% | 3.18% | 0.00% | NA |
| Temperate Japonica | 767 | 95.80% | 0.10% | 1.04% | 3.00% | NA |
| Tropical Japonica | 504 | 78.60% | 2.80% | 8.53% | 10.12% | NA |
| Japonica Intermediate | 241 | 76.30% | 2.10% | 5.81% | 15.77% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 1.10% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0721993438 | G -> DEL | LOC_Os07g36710.1 | N | frameshift_variant | Average:25.719; most accessible tissue: Minghui63 root, score: 49.234 | N | N | N | N |
| vg0721993438 | G -> A | LOC_Os07g36710.1 | synonymous_variant ; p.Gly795Gly; LOW | synonymous_codon | Average:25.719; most accessible tissue: Minghui63 root, score: 49.234 | N | N | N | N |