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GATK BaseRecalibrator

After running BaseRecalibrator we got :
INFO 12:01:19,574 TraversalEngine - 1493749 reads were filtered out during traversal out of 5418149 total (27.57%)
INFO 12:01:19,574 TraversalEngine - -> 824329 reads (15.21% of total) failing NotPrimaryAlignmentReadFilter
INFO 12:01:19,574 TraversalEngine - -> 558510 reads (10.31% of total) failing UnmappedReadFilter
INFO 12:01:19,574 TraversalEngine - -> 110910 reads (2.05% of total) failing ZeroMappingQualityReadFilter

What does the NotPrimaryAlignmentReadFilter, UnmappedReadFilter means?

I could figure out that mapping quality zero which means they're mapped but with zero confidence, so are useless.

Does it implies that there is problem in alignment?



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