| Variant ID: vg1101255292 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1255292 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 241. )
ATACAAGTTTTTCCATTCAATAAATAAATTTACTATAATAGTTGTTTTCTTGACATATCTGTTAGATACTGAGCAAGATGTAATTGAACGAGTCCAGGTG[C/T]
AGAGTTTGAATGGTACCTTACAAAATGGTATGCACGATAATTCAACTATCATTTGTTTAATTCATATCTAGAGTTCATATTTTTATGTTTATCTAATTTG
CAAATTAGATAAACATAAAAATATGAACTCTAGATATGAATTAAACAAATGATAGTTGAATTATCGTGCATACCATTTTGTAAGGTACCATTCAAACTCT[G/A]
CACCTGGACTCGTTCAATTACATCTTGCTCAGTATCTAACAGATATGTCAAGAAAACAACTATTATAGTAAATTTATTTATTGAATGGAAAAACTTGTAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.60% | 2.70% | 5.33% | 51.33% | NA |
| All Indica | 2759 | 11.60% | 0.10% | 6.52% | 81.73% | NA |
| All Japonica | 1512 | 89.40% | 7.10% | 1.46% | 2.12% | NA |
| Aus | 269 | 62.80% | 5.20% | 6.69% | 25.28% | NA |
| Indica I | 595 | 11.60% | 0.00% | 7.73% | 80.67% | NA |
| Indica II | 465 | 7.30% | 0.00% | 4.30% | 88.39% | NA |
| Indica III | 913 | 8.30% | 0.10% | 5.37% | 86.20% | NA |
| Indica Intermediate | 786 | 18.10% | 0.30% | 8.27% | 73.41% | NA |
| Temperate Japonica | 767 | 93.10% | 2.90% | 2.48% | 1.56% | NA |
| Tropical Japonica | 504 | 95.40% | 2.40% | 0.00% | 2.18% | NA |
| Japonica Intermediate | 241 | 64.70% | 30.30% | 1.24% | 3.73% | NA |
| VI/Aromatic | 96 | 31.20% | 4.20% | 27.08% | 37.50% | NA |
| Intermediate | 90 | 53.30% | 1.10% | 6.67% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101255292 | C -> T | LOC_Os11g03340.1 | stop_gained ; p.Gln100*; HIGH | stop_gained | Average:4.679; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1101255292 | C -> DEL | LOC_Os11g03340.1 | N | frameshift_variant | Average:4.679; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |