htseq-out reduced number of the reads in the output sam file

[capricy]

Hello, there,

My htseq-count version: HTSeq-0.5.4p1

My input is a name sorted sam file:
===
HWI-ST514:143982632:C37PRACXX:7:2316:9998:87373 73 A1.0_Cont232 361849 50 47M56N6M * 0 0 GTATTGACCGTTTGACCATGATCCTCACTGACAGTAACAATATCAAGGACGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII MD:Z:53 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XO:i:0 AS:i:0 XS:A:+
HWI-ST514:143982632:C37PRACXX:7:2316:9998:94380 73 A1.0_Cont5 87069 50 47M66N18M * 0 0 TCCACAGCATGGCTGGAGCTGTTCAAGCGAAGTCTTACAGCCCTTTGATGGGCTTGCTCTACGTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII MD:Z:30C34 XG:i:0 NH:i:1 NM:i:1 XM:i:1 XO:i:0 AS:i:-6 XS:A:+
HWI-ST514:143982632:C37PRACXX:7:2316:9999:32498 153 A1.0_Cont103 405380 50 28M477N30M * 0 0 CAGAAAGCACAGTGTTGGCGTAGAGGTCCTTTCTGATATCAACGTCGCACTTCATGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII MD:Z:58 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XO:i:0 AS:i:0 XS:A:-
==

the command line is:

htseq-count -s no -a 10 -t coding_exon -i Parent -o nameSorted.accepted_hits.bam.sam.htseq.exon.sam nameSorted.accepted_hits.bam.sam a.gff

The I counted the reads in both nameSorted.accepted_hits.bam.sam, and nameSorted.accepted_hits.bam.sam.htseq.exon.sam, and found they did not tally:

grep "HWI" nameSorted.accepted_hits.bam.sam.htseq.exon.sam|cut -f5|sort|uniq -c
24579 0
165936 1
344984 3
2533416 50
grep "HWI" nameSorted.accepted_hits.bam.sam|cut -f5|sort|uniq -c
24579 0
165936 1
344984 3
2605593 50

It looks like the new sam file: nameSorted.accepted_hits.bam.sam.htseq.exon.sam, lost many reads with
quality score of 50

Could anyone tell me why?

Thank you very much for your time!