Why my base-quality in alignment is not perfect?
When fasta reads are aligned they are by default assigned the phred score of 40, which in phred+33 encoding is represented by I. Phred+33 uses ASCII characters from ! to I:

!"#$%&amp;'()*+,-./0123456789:;&lt;=&gt;?@ABCDEFGHI


Phred+33 was originally used by sanger machines but it is now used by all popular platforms such as Illumina, Ion-torrent (also Ion-proton) and Roche 454. Since most platforms now use phred+33, most aligners also assume it by default. You can specify other quality encoding formats if you want (such as phred+64 or Solexa).

Have a look at wikipedia page on FASTQ format for the different quality encoding formats.