| Variant ID: vg0721993450 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 21993450 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 327. )
TACATTGGTGGAATGGGCCCTATTGGGCTGAAATACACACGCCTACACTCAACACTCCCCCTCAAGATGGGCGATAAATATCTATCATGCCCATCTTGCT[A/G]
CACGAAGAAGTGCACTCTCTAGCACCTAATGCCTTCGTTAAACTATCAGCTACTTGTTCACCAGAGTTTACAAAGCCTAAGTTTAAGGTTCCCTCATCCA
TGGATGAGGGAACCTTAAACTTAGGCTTTGTAAACTCTGGTGAACAAGTAGCTGATAGTTTAACGAAGGCATTAGGTGCTAGAGAGTGCACTTCTTCGTG[T/C]
AGCAAGATGGGCATGATAGATATTTATCGCCCATCTTGAGGGGGAGTGTTGAGTGTAGGCGTGTGTATTTCAGCCCAATAGGGCCCATTCCACCAATGTA
| 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 | 95.70% | 0.60% | 3.20% | 0.51% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.04% | NA |
| All Japonica | 1512 | 86.80% | 1.70% | 9.99% | 1.52% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.40% | 0.00% | 0.22% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 95.70% | 0.30% | 3.13% | 0.91% | NA |
| Tropical Japonica | 504 | 77.80% | 3.00% | 18.45% | 0.79% | NA |
| Japonica Intermediate | 241 | 77.60% | 3.30% | 14.11% | 4.98% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0721993450 | A -> DEL | LOC_Os07g36710.1 | N | frameshift_variant | Average:24.765; most accessible tissue: Minghui63 root, score: 47.894 | N | N | N | N |
| vg0721993450 | A -> G | LOC_Os07g36710.1 | synonymous_variant ; p.Cys791Cys; LOW | synonymous_codon | Average:24.765; most accessible tissue: Minghui63 root, score: 47.894 | N | N | N | N |