How does bfc assign quality scores?

[danshu]

After error correction, I noticed that some quality scores are strange:
?????????????????????????????????????????????????????????????????????????????????????????????+????????+???????????+?????????????

[sklages]

Phred+33 (Sanger/Illumina) regular quality values, ?=30, +=10. Looks not that strange IMHO.

[danshu]

I checked the quality scores of 1 read before and after error correction.
Before:
33AAA/FBCEGGGEFGGGGGGGGFFGF:FFFFGG>FGGGGED@1FG1=<>C/EECGGGCEGECF:FGGC@FFBFF@C<F</<0CEGFB@CG08@FGGGGGGG@GE;<F=FCG0..8@/DGG
After: the header is ec:Z:0_0:2_0_1:1_0
++???+?????????????????????????????????????+??+????+??????????????????????????????+?+??????????+?????????????"??????+++??+???

So according to the header, only 1 error was corrected in this read, but the quality scores of most bases have been changed.

[danshu]

It seems that the quality scores of most bases were lower after error correction.