Hello everyone,
I am currently analyzing WGS data generated using the Ultima Genomics platform (approx. 200 samples).
During the QC process, I noticed an unexpectedly wide range in the % of mappable reads (calculated from de-duplicated reads):
About 1/3 of the samples show good mappability (>90%).
However, another 1/3 of the samples show significantly low mappability (<70%).
Is this high variance and the presence of low-mappability samples considered a characteristic of the Ultima platform (perhaps due to its specific error profile)? Or does this suggest potential issues such as contamination or library preparation failures in those specific batches?
Any insights or shared experiences with Ultima data would be greatly appreciated.
Thank you.
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SeoG •
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Check the quality of the starting material and the library profiles for samples with less than 70% mapping. Start with the sample concentration, 260/280 ratio, library concentration, and the fragment analyser profile of the libraries.
Very unlikely it has anything to do with Ultima's platform. Most likely a library/sample issue.
I'd check for contamination.