GC pauses are mostly expected when there is frequent eviction from block cache( with un-repeated or large scans loading new blocks in cache everytime, with frequent compaction, with scans on table which is not well distributed across regionservers making one regionserver's cache hot etc. ). PS:- It is not necessary that phoenix always use skip-scan filter for every query for eg:- it will not use it if you don't have leading columns of the rowkey in your "where" clause as it will not know to which key to seek.
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