# of reported mapped reads in stdout does not match # of mapped reads in sam file #53
Description
What steps will reproduce the problem?
1. mapping 50 bp single end illumina reads to bacterial genome
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What is the expected output? What do you see instead?
reported mapped # of reads does not match mapped number of reads in sam file
What version of the product are you using? On what operating system?
Version: 0.3.9 Linux/ubuntu
Please provide any additional information below.
I wanted to ask about a discrepancy I might be seeing in the reported mapping number. When I map to my reference genome I get Mapped#, 20240841. However, when I do samtools idxstats or htseq-count on the reads I end up with 24500246 total reads mapped in that file. Why the huge discrepancy?
Original issue reported on code.google.com by nathan.w...@gmail.com on 31 May 2012 at 4:39