Read discarded

[asdcid]

Hi,

I mapped my paired-end reads to the genome using: ngm -t $threads -p -b -r $ref -1 $in1 -2 $in2 -o $outputFile

and I found the log said: [MAIN] Done (933226 reads mapped (83.79%), 180582 reads not mapped (30 discarded), 1113778 lines written)(elapsed: 55.646282s)

I am not sure why some reads were discarded?

In addition, I mapped the sam dataset to another reference, and the number of discarded reads is different. It makes me confuse.

[MAIN] Done (931410 reads mapped (83.62%), 182398 reads not mapped (16 discarded), 1113792 lines written)(elapsed: 61.987221s)