The CDS (coding sequence) name or gene name is shown in yellow, i.e. It indicates that base call Phred quality scores are high and that we have high confidence that reads are mapped to the correct location and orientation relative to the reference genome. The Geneious mapping algorithm computes and assigns a mapping quality metric for each sample read. 2 every 150 bp (basepair) read is shown in green. Sample Read Quality Scoresĭrilling down somewhat around a particular locus shows individual sample reads mapped to the reference genome. We can Blast these unmapped reads against phage databases and plasmid databases for species identification. When sequence alignment is finished, there may be a significant number of unmapped reads, which often represent inserted phage and/or plasmid sequences. These are commonly seen in bacterial sequences and in most cases represent bacteriophage, prophage, and plasmid insertions. This level of coverage often yields the uniform coverage seen in this example.Īlso, note the distinct gap around locus 4,100,000. Using tools like the Illumina Sequence Coverage Calculator, our own internal coverage calculators, and extensive experience with bacterial sequencing projects, we usually recommend a minimum of 100X coverage. Note the uniform coverage across the entire reference genome. = 22.6 reads and pairwise identity = 99.3%. coli sample was aligned to the reference strain with the Geneious Prime mapping algorithm. A total of 6,346,413 reads (DNA fragments) from the E. coli bacterial sample aligned to the reference genome E.

We then perform sequence alignments of the FastQ files against the reference genomes. Our client researchers generally choose appropriate reference genomes for their projects, although we may assist them in identifying proper genomes. When sequencing runs are finished, our sequencers generate raw FastQ files, which typically contain millions of short DNA fragments (“reads”). We often use Geneious for the alignment of sequenced samples to reference genomes.

Geneious convert sequencher spf file