Samtools flagstat with sncRNA (single-end reads)

Question

[Apex92]

Hi, I am analyzing sncRNA reads (single-end) provided by Nextflex sequencing method. I used bowtie with -m 1 option to align the reads to the mouse genome. Then I used HTSeq-count to count the number of reads assign to each feature. I get low counts in HTSeq-count and I do not know this is because of the alignment or the HTSeq-count (I did not specify -s option so the default was yes).

And when I run samtools flagstat file.bam on one of the bam samples I get these output.

733523 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
346170 + 0 mapped (47.19% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

I am very new to these kinds of analyses so could someone please help me to understand if the alignment is correct or not and there if is any problem with HTSeq-count to be solved e.g. -s option? Many thanks