| Variant ID: vg0815412275 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 15412275 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )
CCTGCTGCAACACCTGATGGTACTGTTGCTGCATCTGTTGCATCATCATTGTCATCATCTGAGTCTGATTGTCCAACACCTGAGCAATTGTTGGGTTCTC[G/A]
GGCGGTGGGGACGGACTGTTGTCAGATGCACCGTTGGCACGTGCTCCATTGGTCGGCTCTTCGCTGCCACTGGCGTTGTTCGAGTCGCGTGAACCATTCC
GGAATGGTTCACGCGACTCGAACAACGCCAGTGGCAGCGAAGAGCCGACCAATGGAGCACGTGCCAACGGTGCATCTGACAACAGTCCGTCCCCACCGCC[C/T]
GAGAACCCAACAATTGCTCAGGTGTTGGACAATCAGACTCAGATGATGACAATGATGATGCAACAGATGCAGCAACAGTACCATCAGGTGTTGCAGCAGG
| 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 | 26.80% | 0.20% | 7.41% | 65.59% | NA |
| All Indica | 2759 | 4.20% | 0.30% | 9.97% | 85.54% | NA |
| All Japonica | 1512 | 60.10% | 0.10% | 1.92% | 37.90% | NA |
| Aus | 269 | 77.30% | 0.00% | 13.75% | 8.92% | NA |
| Indica I | 595 | 1.00% | 0.00% | 1.85% | 97.14% | NA |
| Indica II | 465 | 3.20% | 0.20% | 7.10% | 89.46% | NA |
| Indica III | 913 | 2.60% | 0.80% | 17.09% | 79.52% | NA |
| Indica Intermediate | 786 | 8.90% | 0.10% | 9.54% | 81.42% | NA |
| Temperate Japonica | 767 | 83.70% | 0.10% | 0.91% | 15.25% | NA |
| Tropical Japonica | 504 | 29.80% | 0.00% | 2.98% | 67.26% | NA |
| Japonica Intermediate | 241 | 48.50% | 0.00% | 2.90% | 48.55% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 2.08% | 93.75% | NA |
| Intermediate | 90 | 33.30% | 0.00% | 7.78% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0815412275 | G -> A | LOC_Os08g25330.1 | synonymous_variant ; p.Pro37Pro; LOW | synonymous_codon | Average:11.012; most accessible tissue: Zhenshan97 root, score: 20.427 | N | N | N | N |
| vg0815412275 | G -> DEL | LOC_Os08g25330.1 | N | frameshift_variant | Average:11.012; most accessible tissue: Zhenshan97 root, score: 20.427 | N | N | N | N |