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why do BaseRecalibrator read counts differ?

following on from Pallavi's question "I Don't understand what is filtering out during traversal ", can you explain why the number of processed reads ("INFO 02:09:56,512 BaseRecalibrator - Processed: 1059663038 reads" from Pallavi's example) differs so much from the total number of reads ("INFO 02:09:56,514 MicroScheduler - 25351 reads were filtered out during traversal out of 45356 total"). Do these numbers relate to different sets of reads?

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