| Variant ID: vg0106165909 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 6165909 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 268. )
CCCCAGTATCAACCCACCAATTAGTAGATTGATTAACTGAAAAAACAGTAGGTAAATTACCATACCCGCTTCCATCTCCAGTGTTGCCAATGGTCACATT[A/G]
GCAGACTTAGAAGTCTGCCCTGCAGGTGCCTTCATCCCCTTGCGCTGTGGACACTTCCTAGCCAGATGACCAACTTGGCCACACACAAAGCAAGTCCTCT
AGAGGACTTGCTTTGTGTGTGGCCAAGTTGGTCATCTGGCTAGGAAGTGTCCACAGCGCAAGGGGATGAAGGCACCTGCAGGGCAGACTTCTAAGTCTGC[T/C]
AATGTGACCATTGGCAACACTGGAGATGGAAGCGGGTATGGTAATTTACCTACTGTTTTTTCAGTTAATCAATCTACTAATTGGTGGGTTGATACTGGGG
| 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 | 0.70% | 0.10% | 1.84% | 97.38% | NA |
| All Indica | 2759 | 0.60% | 0.00% | 2.03% | 97.39% | NA |
| All Japonica | 1512 | 0.50% | 0.00% | 1.46% | 98.02% | NA |
| Aus | 269 | 1.10% | 1.90% | 2.23% | 94.80% | NA |
| Indica I | 595 | 0.50% | 0.00% | 0.17% | 99.33% | NA |
| Indica II | 465 | 0.60% | 0.00% | 1.51% | 97.85% | NA |
| Indica III | 913 | 0.20% | 0.00% | 3.18% | 96.60% | NA |
| Indica Intermediate | 786 | 1.00% | 0.00% | 2.42% | 96.56% | NA |
| Temperate Japonica | 767 | 0.50% | 0.00% | 0.39% | 99.09% | NA |
| Tropical Japonica | 504 | 0.80% | 0.00% | 3.77% | 95.44% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 1.04% | 98.96% | NA |
| Intermediate | 90 | 5.60% | 0.00% | 2.22% | 92.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0106165909 | A -> G | LOC_Os01g11450.1 | synonymous_variant ; p.Ala159Ala; LOW | synonymous_codon | Average:7.557; most accessible tissue: Minghui63 flag leaf, score: 12.986 | N | N | N | N |
| vg0106165909 | A -> DEL | LOC_Os01g11450.1 | N | frameshift_variant | Average:7.557; most accessible tissue: Minghui63 flag leaf, score: 12.986 | N | N | N | N |