The Comparison of two genomes was performed with LAST. In order to calculate the weighted Mean and Median of Identity and the Aligned nucleotide fraction, the following steps were taken:

Building Last-Database:

lastdb -P5 -uNEAR -R01 LASTDB-name Target-Assembly

Training LAST for optimal Matrix-parameter:

last-train -P0 --revsym --matsym --gapsym -E0.05 -C2 LASTDB-name Query-Assembly > last-train.mat

Aligning and filtering for unique best alignments of the query:

lastal -m50 -E0.05 -P0 -C2 -p last-train.mat LASTDB-NEAR $1 | last-split -m1 > last-split.maf

Get 1-to-1 alignments:

maf-swap last-split.maf |last-split -m1 | maf-swap > maf-swap.maf

Calculate Aligned nucleotide fraction of query and target:
Sum of Alignmentlength - (Sum of number of gaps + Sum of number of Mismatches)

Calculate Aligned nucleotide fraction of the query (%):
get sum of Alignmentlength (Prefix is specific for the reference genome):

grep -v '^#\|^a\|^p' maf-swap.maf | grep Prefix (eg: "NC_*") | awk '{sum+=$4} END {print sum}'

get sum of number of gaps:

grep -v '^#\|^a\|^p' maf-swap.maf | grep Prefix | grep -o "-" | wc -m

Generate blast tab output from LAST output (blast outfmt 6):

last-postmask maf-swap.maf | maf-convert blasttab | awk -F'=' '$2 <= 1e-5' > last.blasttab

Sum of number of Mismatches:

less last.blasttab | awk '{sum+=$5} END {print sum}'

Calculate Aligned nucleotide fraction of the target (%):
get sum of Alignmentlength:

grep -v '^#\|^a\|^p' maf-swap.maf | grep -v Prefix | awk '{sum+=$4} END {print sum}'

get sum of number of gaps:

grep -v '^#\|^a\|^p' maf-swap.maf | grep -v Prefix | grep -o "-" | wc -m

A whole genome comparison was performed by generating dot plots with GEnome Pair Rapid Dotter (gepard). Dot matrix analysis is a method used to compare two proteins or nucleic acid sequences. Every dot in the dot plot represents an identical element of the compared sequences.