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Old 02-22-2017, 02:26 AM   #2
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 838
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samtools flagstat can only report what's in the file, so if there are no unmapped reads in the BAM file then the calculated mapping rate will be 100% (with some reduction in that due to unpaired and low-quality mappings, if included).
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