Low % reads mapped and high % genome coverage

Question

[natural_decline]

Bacterial isolate sequenced on Illumina platform, fastq's are decontaminated prior to mapping and alignment. Coverage analysis run with samtools and then mapping stats calculated with mapped reads count text file vs total reads count text file. I have a sample with low mapping % (19.85) and high % genome coverage (93.4%). This seems contradictory, can someone help explain this result?

Answer 1

[GenoMax]

This seems contradictory, can somehow help explain this result?

Not necessarily. If you have a lot of data then even at 20% alignment you could end up with high genome coverage (since bacterial genomes are small and you are basically oversampling).

That said, this data sounds heavily contaminated (despite of your assertion that is is decontaminated) if only 20% of it is aligning to the intended target.

[natural_decline]

Thank you, this does make sense