| Variant ID: vg1125679207 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 25679207 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 76. )
TTCATGTCTTACTTATTTTCTAAGTGAGCCGATATAGCTTTGCCCTACCGGCTGGGCTATGACAATGTGTCATCGGTCTGCTGACCGATCGGCCATTGTT[C/T]
TCTGACTTGGTTCACTTGTTTCTTGTTGATTGCAGATCAAATCAACTGGCACGCTCTACTTACGACTAGGCAAGCCATTTGGACCTGCACTGGAGTTAAG
CTTAACTCCAGTGCAGGTCCAAATGGCTTGCCTAGTCGTAAGTAGAGCGTGCCAGTTGATTTGATCTGCAATCAACAAGAAACAAGTGAACCAAGTCAGA[G/A]
AACAATGGCCGATCGGTCAGCAGACCGATGACACATTGTCATAGCCCAGCCGGTAGGGCAAAGCTATATCGGCTCACTTAGAAAATAAGTAAGACATGAA
| 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 | 41.20% | 28.70% | 12.04% | 18.05% | NA |
| All Indica | 2759 | 37.50% | 32.10% | 10.55% | 19.79% | NA |
| All Japonica | 1512 | 50.40% | 22.40% | 13.56% | 13.62% | NA |
| Aus | 269 | 36.80% | 19.70% | 13.75% | 29.74% | NA |
| Indica I | 595 | 67.40% | 7.10% | 8.40% | 17.14% | NA |
| Indica II | 465 | 43.90% | 13.50% | 16.34% | 26.24% | NA |
| Indica III | 913 | 17.00% | 60.20% | 8.54% | 14.24% | NA |
| Indica Intermediate | 786 | 35.10% | 29.40% | 11.07% | 24.43% | NA |
| Temperate Japonica | 767 | 70.70% | 11.30% | 11.86% | 6.13% | NA |
| Tropical Japonica | 504 | 25.40% | 34.70% | 15.48% | 24.40% | NA |
| Japonica Intermediate | 241 | 38.20% | 32.00% | 14.94% | 14.94% | NA |
| VI/Aromatic | 96 | 12.50% | 58.30% | 22.92% | 6.25% | NA |
| Intermediate | 90 | 41.10% | 26.70% | 15.56% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1125679207 | C -> T | LOC_Os11g42640.1 | upstream_gene_variant ; 1452.0bp to feature; MODIFIER | silent_mutation | Average:10.964; most accessible tissue: Callus, score: 21.753 | N | N | N | N |
| vg1125679207 | C -> T | LOC_Os11g42650.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.964; most accessible tissue: Callus, score: 21.753 | N | N | N | N |
| vg1125679207 | C -> DEL | N | N | silent_mutation | Average:10.964; most accessible tissue: Callus, score: 21.753 | N | N | N | N |