Hi,

I have run tophat with the following parameters, specifying each reads can only map once and that they must map concordantly.

 tophat2 --solexa1.3-quals -p 12 -r 80 --read-mismatches 0 --max-multihits 1 --no-mixed --no-discordant

Therefore why do I have to following output in the align_summary.txt. Were the reads that mapped multiply discarded? ​

Left reads:
               Input:  23815106
              Mapped:   9138883 (38.4% of input)
            of these:     92429 ( 1.0%) have multiple alignments (77607 have >1)
Right reads:
               Input:  23844741
              Mapped:   9168518 (38.5% of input)
            of these:     92790 ( 1.0%) have multiple alignments (77715 have >1)
38.4% overall read alignment rate.

Aligned pairs:   7091314
     of these:     10745 ( 0.2%) have multiple alignments
          and:    250038 ( 3.5%) are discordant alignments
28.7% concordant pair alignment rate.

Thanks