Table 4 presents the OLS, SAR and SEM model results using a spatial weight matrix based on queen contiguity, while Table 5 presents SAR and SEM models using the inverse distance matrix.
We computed standard contiguity metrics (Table 1) for all assemblies.
Accordingly, we ran our tool iteratively 30 times and at each instance increased the distance between k-mer pairs from 500 to 16,000 bp, thus gradually improving the long-range contiguity of the assembly (Table 1F, Additional file 1: Figure S4).
This was likely due to the poorer contiguity (as indicated by N50, Table 1) of the M. acridum genome assembly, which would prevent whole-genome scale synteny from being accurately observed.
Final assemblies were chosen to maximize contiguity and completeness while minimizing redundancy (table 2).
Table 3 shows several contiguity, coverage and quality metrics computed using the same reference genome and QUAST command-line for the three assemblies.
Contiguity and length varied over a broad range (Table 3; additional file 1: Table S1).
With the assistance of annotation, the chimerism rate dropped to 4.5 % and the contiguity rate naturally rose to 100%% [Table 1, Additional file 11].
Five repeats we found of length five or greater were biologically significant, in that they would preserve protein-coding information if they were to function in IES removal, and they also satisfy other criteria such as rarity in the sequence and linear contiguity in a single macronuclear-destined segment (Table 2).
As an attempt to perform a fair comparison, we increased the value of k from 27 to 51 for the assembly done in Table 2 (k = 56 showed worse contiguity).
