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Table 2 Read error profiles for Giardia AWB and Giardia BGS MinION sequencing runs

From: Benchmarking hybrid assemblies of Giardia and prediction of widespread intra-isolate structural variation

Error type/readsAWB_0150AWB_0157AWB_2331AWB_2338BGS_2237BGS_2244
Proportion of reads counted (%)87.5583.5628.0452.6112.6277.47
Overall base identity (%)76.90774.57754.29365.90458.25556.636
Overall base identity error rate (%)23.09325.42345.70734.09641.74543.364
Aligned base identity (%)90.52689.35283.07683.91591.42989.954
Aligned base identity error rate (%)9.47410.64816.92416.0858.57110.046
Identical bases per 10080.43078.33871.02471.59780.85578.834
Inserted bases per 1005.2913.8817.8115.0873.4734.478
Deleted bases per 1005.8608.4506.7589.5928.1057.886
Substitutions per 1008.4159.33414.40613.7257.5698.801
Mean insertion1.6381.4621.7551.4801.4821.530
Mean deletion1.6211.7871.5911.7881.8481.898
  1. Notes: Using NanoOK [26], 1D reads were aligned to the corresponding reference genome and the error profiles of aligned reads were evaluated. NanoOK outputs read error profiles for each reference contig. To obtain overall error profiles for all reads, the values for each contig were multiplied by the proportion of total reads that aligned to that contig. The sum of these values for each error metric were scaled according to the proportion of total sequencing reads that were used for NanoOK’s analysis