bowtie2, option -N

[bye]

We have SE 100bp reads aligned with bowtie2. We noticed that when keep other options the same, but change -N 0 to -N 1, we got some really different alignments, see example below:

bowtie2 -x ./hg19/hg19_all --end-to-end -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 --score-min L,-1,-1 -c AGAGCTGTTCCTATTCGGCCATCTTGGCTCCTCCTCCCGGATTCACTGATTTTTTGAAGGGTTTTTTGTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTT

Output:

0       0       chr4    58434477        42      101M    *       0       0       AGAGCTGTTCCTATTCGGCCATCTTGGCTCCTCCTCCCGGATTCACTGATTTTTTGAAGGGTTTTTTGTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTT  IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII  AS:i:-12        XN:i:0  XM:i:2  XO:i:0  XG:i:0  NM:i:2  MD:Z:0G72T27    YT:Z:UU

bowtie2 -x ./hg19/hg19_all --end-to-end -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --score-min L,-1,-1 -c AGAGCTGTTCCTATTCGGCCATCTTGGCTCCTCCTCCCGGATTCACTGATTTTTTGAAGGGTTTTTTGTGTCTCTATCTCCTTCAGTTCTGCTCTGATCTT

Output:

0       16      chr2    136138378       0       60M5I1M1I34M    *       0       0       AAGATCAGAGCAGAACTGAAGGAGATAGAGACACAAAAAACCCTTCAAAAAATCAGTGAATCCGGGAGGAGGAGCCAAGATGGCCGAATAGGAACAGCTCT  IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII  AS:i:-88        XN:i:0  XM:i:10 XO:i:2  XG:i:6  NM:i:16 MD:Z:13C11C3A8C18T5C2T0T11A14C0
        YT:Z:UU

I'm confused about the results. I thought -N 1 should be able to pick up the best alignment with -N 0, how come the alignment results are so much worse when -N 1 for the same read?

Thanks in advance!