![]() Provides counts for each of 13 categories based primarily on bit flags in the FLAG field. With mate mapped to a different chr (mapQ>=5) 0x1 bit set and neither 0x4 nor 0x8 bits set and MRNM not equal to RNAME and MAPQ >= 5) With mate mapped to a different chr 0x1 bit set and neither 0x4 nor 0x8 bits set and MRNM not equal to RNAME Singletons both 0x1 and 0x8 bits set and bit 0x4 not setĪnd finally, two rows are given that additionally filter on the reference name (RNAME), mate reference name (MRNM), and mapping quality (MAPQ) fields: With itself and mate mapped 0x1 bit set and neither 0x4 nor 0x8 bits set Properly paired both 0x1 and 0x2 bits set and 0x4 bit not set ![]() ![]() Which would indicate that there are a total of 150 reads in the input file, 122 of which are marked as QC pass and 28 of which are marked as “not passing quality controls”įollowing this, additional categories are given for reads which are: For example:ġ22 + 28 in total (QC-passed reads + QC-failed reads) The first row of output gives the total number of reads that are QC pass and fail (according to flag bit 0x200). In the default output format, these are presented as “#PASS + #FAIL” followed by a description of the category. Each category in the output is broken down into QC pass and QC fail. Does a full pass through the input file to calculate and print statistics to stdout.
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