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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?