We checked all Illumina reads for quality, and removed sequence reads containing ''Ns''. Custom perl script was written to convert Illumina reads into fastq format. The script ''fq_all2std.pl'' from MAQ [40] converted fastq format to Sanger fastq format. Reads in sanger fastq format, were mapped onto the Histophilus somni 2336 genome sequence (GenBank Accession number. CP000947) using the alignment tool Bowtie [41] , allowing for a maximum of two mismatches. The reads that mapped to more than one location were discarded. We used Samtools [42] to convert data into SAM/BAM format, and to generate alignment results in a pileup format. Pileup format provides the signal map file and has per-base format coverage. Custom perl scripts were written to calculate the background expression. Processed data was deposited in GEO with the accession number GSE29578.