| Variant ID: vg0139404672 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39404672 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 117. )
AGTCGACGCCCGGGCGCTGGTTAAACCCGCGAACCACCCAACGTGCCTTGTACTTGTCGAGTGAGCCGTCAGCATGAAGCTTGGTCTTGAAGACCCACTT[G/A]
CCGGTGATGATCCGAGCACCGGGAGGCCGGGGAACCAGAGTCCACGTCCTGTTCGCGAGCAGGGCGTCGAACTCAGCCTGCATCGCCGCGCGCCAGTTGG
CCAACTGGCGCGCGGCGATGCAGGCTGAGTTCGACGCCCTGCTCGCGAACAGGACGTGGACTCTGGTTCCCCGGCCTCCCGGTGCTCGGATCATCACCGG[C/T]
AAGTGGGTCTTCAAGACCAAGCTTCATGCTGACGGCTCACTCGACAAGTACAAGGCACGTTGGGTGGTTCGCGGGTTTAACCAGCGCCCGGGCGTCGACT
| 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 | 29.20% | 0.70% | 1.52% | 68.58% | NA |
| All Indica | 2759 | 1.90% | 0.00% | 2.03% | 96.09% | NA |
| All Japonica | 1512 | 85.10% | 2.10% | 0.40% | 12.43% | NA |
| Aus | 269 | 0.70% | 0.00% | 2.23% | 97.03% | NA |
| Indica I | 595 | 2.90% | 0.00% | 1.85% | 95.29% | NA |
| Indica II | 465 | 1.50% | 0.00% | 1.51% | 96.99% | NA |
| Indica III | 913 | 0.80% | 0.00% | 1.53% | 97.70% | NA |
| Indica Intermediate | 786 | 2.70% | 0.00% | 3.05% | 94.27% | NA |
| Temperate Japonica | 767 | 94.30% | 3.70% | 0.52% | 1.56% | NA |
| Tropical Japonica | 504 | 70.20% | 0.60% | 0.40% | 28.77% | NA |
| Japonica Intermediate | 241 | 86.70% | 0.40% | 0.00% | 12.86% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 0.00% | 98.96% | NA |
| Intermediate | 90 | 44.40% | 0.00% | 4.44% | 51.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139404672 | G -> A | LOC_Os01g67800.1 | synonymous_variant ; p.Gly938Gly; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0139404672 | G -> DEL | LOC_Os01g67800.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |