Hello everyone, so I am a student and I am doing my final project for Next-generation sequencing using Galaxy server. After generating the FASTQC files to detect the quality of my reads, I noticed that I had many reads at the end of the graph in the red region (bad quality), so I used trimmomatic operations (Slidingwindow+ CROP). When I did a FASTQC for the new trimmed reads, I see that most of them are in the green region, but without the yellow boxes, they are all represented with the black whiskers, so I got worried that I have done something wrong or I trimmed a lot of data. Then I continued with mapping with BWA-MEM, merged the BAM files, and then generated mpileup files so I can call the SNPs, my pileup file also looked weird to me and I wasn't sure if that is correct or I faced some problems. I will show a part how my pileup file turned out at the end of the post.
I would really appreciate if someone help me and tell me that I am in the right track, or I did something wrong. Thank you :)

1   2   3   4   5   6
chr1    9999    N   1   ^!C ;
chr1    10000   N   1   A   /
chr1    10001   t   6   .^!.^!.^!.^!.^!.    ?AAAA/
chr1    10002   a   18  ......^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.  AAAAAAAA6A/A6A/AAA
chr1    10003   a   21  ..................^!.^!.^!. AAAAAAAAAAAAAAAAAAAA/
chr1    10004   c   30  .....................^!.^!.^!.^!.^!.^!.^!.^!.^!.    EAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
chr1    10005   c   31  ..............................^!.   EAAAAAAAAAAAAAAAAAAAAAAAAAAAAA>
chr1    10006   c   39  ...............................^!.^!.^!.^!.^!.^!.^!.^!. EEEEEEAAAAAAAAAAA/AAAAAAAAAAAA>AAAAAAAA
chr1    10007   t   42  .......................................^!.^!.^!.    AEEEEEEAEAEEEEEEAEAAAAAAAAAAAAAAAAAAAAA6A/
chr1    10008   a   47  ..........................................^!.^!.^!.^!.^!.   AEEEAEEEEAEEEEEEEEEEEAAAAAAAAAAAAAAAAAAAAAAA6AA
chr1    10009   a   50  ................................................^!.^!.  EAE/EEEAEEEEEEEAEEEEEAEEAAAEEEAAAAAAAAAAAA6AA6A///
chr1    10010   c   66  ..................................................^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.  EEEEAEEEEEEEEEEEAAEEEEAEEEEAEEEAAAAAAAAAAAAAAAA3AA/AAAA/A/AAAAAAAA
chr1    10011   c   69  ..................................................................^!.^!.^!. AEEEEEEEAAEEEAEEEEEEEEEEEEAEEEEEEEEEAEEAAAAAAAA>AAAAAAAAAAAAAAAAAA>>>
chr1    10012   c   81  .....................................................................^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.   AEEEAEAEEEEEEEEEAEEEEEAEAEAAEEEEEEEEEEEAE/AAAAAAAAAAAAAAAAAAAAAAAA>>>AAAAAAA6A6AA
chr1    10013   t   82  .................................................................................^!.    AEAEEEEEAAEAEAEEEAEEEA/EAEEAEEAEEEEEEEE/EEAAEAEAAAAAAAAAA/AAAA/A/AAAAAAAAA/A/AAAAA
chr1    10014   a   96  ..................................................................................^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.    AEEEEEEEEEEEEEEEEEEEEE/EEEEAEEEEEEEEEEEEEEEAEAECEEAAAAAAAAAAAA/AA/AAAAAAAA/A66A6AAAA6666AAAA/6/A
chr1    10015   a   98  ................................................................................................^!.^!.  AEEEEEEEEAEEEEEEEEEAEAEAEAAE6EAEAAEAE6EA6/AEEAECEE/EEAE/E/AAEEAE/AAAAAAAA/AAAAAAAAAAAAAAAAAAAAAAAA
chr1    10016   c   108 ..................................................................................................^!.^!.^!.^!.^!.^!.^!.^!.^!.^!.