I stumbled upon this problem when playing with different flags of bowtie. I am not sure whether this is a bug or not. I extracted a read from my dataset (shown below) and put that in a file (test.fastq). It is in Sanger Fastq format.

@SRR218096.75 HWUSI-EAS465:3:1:3:839 length=36
ACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+SRR218096.75 HWUSI-EAS465:3:1:3:839 length=36
..1>@<.;>2>@@>2;@>;@@@@@@;@@@@;@BBBA

Then I used the following command to map this read to Arabidopsis Tair10 genome. I made the index by using:

bowtie-build tair10.fasta TAIR10

tair10.fasta is just a concatenated file of *.fas from ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/. Then map:

bowtie -a -m 25 -n 3 -e 60 --best --strata --sam TAIR10 test.fastq test

The alignment output is:

SRR218096.75 16 Chr3 2094491 255 36M * 0 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGT ABBB@;@@@@;@@@@@@;>@;2>@@>2>;.<@>1.. XA:i:2 MD:Z:7C21T5G0 NM:i:3
SRR218096.75 16 Chr3 2094494 255 36M * 0 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGT ABBB@;@@@@;@@@@@@;>@;2>@@>2>;.<@>1.. XA:i:2 MD:Z:4C21T8G0 NM:i:3
SRR218096.75 16 Chr3 2094504 255 36M * 0 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGT ABBB@;@@@@;@@@@@@;>@;2>@@>2>;.<@>1.. XA:i:2 MD:Z:16T11A7 NM:i:2

However, by manually checking the sum of sequencing qualities in mismatched positions, I found the second alignment result with "4C21T8G0" actually has the sum exceeding 60, although I specified -e 60. ASCII code representing sequencing qualities in 3 mismatched positions are "@", "2" and "." . They correspond to 31, 17 and 13 in quality score. So the sum is 61 despite of -e 60. Please let me know if I made a mistake somewhere.

I am using bowtie 0.12.8.