Table 1.
Statistics of the completeness of the hybrid de novo assembly genome of ‘Golden Delicious’ based on 248 core eukaryotic genes, produced by the software CEGMA [7] with default parameters
| Group | #Prots | %Completeness | #Total | Average | %Ortho |
|---|---|---|---|---|---|
| Complete | 231 | 93.15 | 545 | 2.36 | 74.46 |
| Group1 | 63 | 95.45 | 127 | 2.02 | 66.67 |
| Group2 | 50 | 89.29 | 120 | 2.40 | 78.00 |
| Group3 | 58 | 95.08 | 136 | 2.34 | 72.41 |
| Group4 | 60 | 92.31 | 162 | 2.70 | 81.67 |
| Partial | 243 | 97.98 | 710 | 2.92 | 86.01 |
| Group1 | 64 | 96.97 | 173 | 2.70 | 82.81 |
| Group2 | 54 | 96.43 | 159 | 2.94 | 87.04 |
| Group3 | 61 | 100.00 | 181 | 2.97 | 88.52 |
| Group4 | 64 | 98.46 | 197 | 3.08 | 85.94 |
#Prots: number of 248 ultra-conserved CEGs present in genome
%Completeness: percentage of 248 ultra-conserved CEGs present
Total: total number of CEGs present including putative orthologs
Average: average number of orthologs per CEG
%Ortho: percentage of detected CEGS that have more than 1 ortholog
‘Complete’: predicted proteins in the set of 248 CEGs that, when aligned to the HMM (a hidden markov model) for the KOG (eukaryotic orthologous groups) for that protein family, give an alignment length that is at least 70 % of the protein length
‘Partial’: If a protein is not complete, but exceeds a pre-computed minimum alignment score, then we call the protein ‘partial’. The pre-computed scores are all in the file CEGMA/data/completeness_cutoff.tbl [7]
CEGs: core eukaryotic genes