I mapped several simulated reads with novoalign in its default reporting mode (-o SAM -o fullNW -e 1 --ILQ_QC) and asking it to report multiple hits (-o SAM -o fullNW -r A 20 -q 5). I got several reads for which the multiple hit mode gives only one hit, and the default mode does not report it. indicating multiple hits. I have attached an example of such reads. Can you please explain the reason for this? Could it be that novoalign does not report multiple hits if there are too many of them?
Mapping reported under default mapping
893 4 * 0 0 * * 0 0 caataaacatatgtgtgcatgtgtctttatagcagcatgatttatagtcctttgggtatatacccagagagggga >=:7@>7=>??4'>8D9?6'3@C5;4?>68.@5=:7@>7=>??4'>8D9?6'3@C5;4?>68.@5