Read length mismatch between bam and query reads

Question

[蓝寒]

Hi all,

I met a problem when mapping Pacbio Iso-seq reads.

I got ccs reads and corrected by NGS data, but when I use GMAP located in SMRTlink, I found that:

The length of reads I extracted from bam file 'SEQ' list are longer than query sequences I submitted.

Which means that, for example, I use 1k read 'AA' to map reference but the 'SEQ' length of AA in bam is 1.2k.

I just wonder why, I have checked previous questions but didn't get accurate result, is that due to full-length? Some answer speak of Insertion or trim, but that should be query longer than bam ?

Thanks all!