alignment result

Question

[ahmad.sajad4541]

Hello guys, I have used hisat2 for alignment of one of my sample to reference genome. This is the actual alignment result. can anyone please guide me if the alignment result is correct or not. Since I have the the fastqc results which showed me red flag for Per Base Sequence Content and sequence duplication level for almost all sample. Since these red flags are common for rna-seq data so I moved to the alignment step without trimming the data, and the results of hisat2 alignment is given below

Per base sequence content:

sequence level duplication:

22992278 reads; of these:
  22992278 (100.00%) were paired; of these:
    1769189 (7.69%) aligned concordantly 0 times
    20386810 (88.67%) aligned concordantly exactly 1 time
    836279 (3.64%) aligned concordantly >1 times
    ----
    1769189 pairs aligned concordantly 0 times; of these:
      223692 (12.64%) aligned discordantly 1 time
    ----
    1545497 pairs aligned 0 times concordantly or discordantly; of these:
      3090994 mates make up the pairs; of these:
        2272245 (73.51%) aligned 0 times
        750748 (24.29%) aligned exactly 1 time
        68001 (2.20%) aligned >1 times
95.06% overall alignment rate
62 minutes and 44 seconds elapsed.

[GenoMax]

20386810 (88.67%) aligned concordantly exactly 1 time

This result is fine.

[ahmad.sajad4541]

Thank you so much. Should i proceed for annotation step?