Right clicking on the panel that is displaying the variation data provides a number of options including filtering and different colour schemes. For single base changes the colour represents the base it is being changed to, i.e. There are also some other points of interest вЂ“ the gene has independently become a pseudogene in a second strain, because of a SNP leading to a premature stop codon, and a third strain actually has a recombination that spans this whole region (shown by the increased SNP density). The magenta insertions in most strains show where this frame shift has been caused by a deletion in the reference strain (and one of the other strains). The pspA gene in the reference is a pseudogene as a result of a frame shift. This shows the variation data for 11 strains of this compared to the reference. Example 4: Streptococcus pneumoniaeДЄ region of Streptococcus pneumoniae antibiotic resistant pandemic clone PMEN1.

Mycobacterium tuberculosis H37Rv genome showing Illumina re-sequencing data. Sequencing errors produce randomly distributed lines and true SNPs can be seen where lines align vertically. Additionally a SNP density plot can be shown (вЂGraphвЂ™ -> вЂSNPвЂ™). Right clicking on the BAM view gives an option to вЂShowвЂ™ -> вЂSNP marksвЂ™ and vertical red lines on the reads indicate differences to the reference. Mycobacterium tuberculosis H37Rv genome example with Illumina re-sequencing data. Example 3: Mycobacterium tuberculosis H37Rv

Bam file format example