Feature SAM-Profiler SamStat FastQC Operative System L/W/M L L/W/M Graphical UI Yes No Yes Programming Language C# C Java External Dependencies .Net/Mono Runtime Noa Java Runtime Input SAM/BAM SAM/BAM SAM/BAM Batch Input Yes Yes No Interactive Graphical Output Yes No No Parallel programming Yes No Yes Read Quality Yes Yes Yes Mapping Quality Yes Yes No Per-Read Read Quality Yes No No Per-Base Read Quality Yes No Yes Per-Chromosome Read Quality Yes No No Nucleotides Overrepresentation No Yes Yes Duplicates Yes No Yesb Per-Chromosome Duplicates Yes No No Exonic/Intronic/Intergenic Coverage Yes No No Exonic Fold-Coverage Yes No No Fragment Size Distribution Yes No No Perfectly/Imperfectly Mapped Reads Yes No No Properly/Improperly Pairs Yes No No M/U and U/U Pairs Yes No No Improperly Mapped Reads Analysis Yes No No Mismatch Distribution Yes Yes No Per-Read CG Distribution Yes No Yes A,C,T,G,N Distribution Yes Yes Yes L/W/M: Linux/Windows/MacOS. a: Requires installation. b: Duplicates calculated only for the first 200000 reads.

Table 1: Summary of the main characteristics of three SAM/BAM reporting tools.