Troubleshooting

Sequencing quality

The sequencing quality is not necessarily correct. That's the reason why some alignment software recalculates the quality: GATK.

Technical biais

Bias due to hexamer random priming

This bias impacts the composition of the beginning of the sequences.

Bias due to a contamination

This graph is an example of a GC percent bias that could indicate sample contamination with another organisme or a fragment.