SSAHA2 Mapping Read Count

I have LS454's SFF files. Fastq file only have 133,202 reads(Step 2), but my SSAHA2 result(BAM file) have 188,214 reads(Step 5). Why different?? 1000 genomes data exactly same but my result are different.

1. Run sff_extract(http://bioinf.comav.upv.es/sff_extract/usage.html), I receive the KOBB0909_190.fastq file.

sff_extract -o KOBB0909_190_hong -Q KOBB0909_190.sff

1. FASTQ file have total 133,202( 532808/4)reads.

cat KOBB0909_190_hong.fastq |wc -l 532808

1. Running SSAHA2 like this

ssaha2 -454 -output sam -outfile KOBB0909_190.sam -diff 10 -best 1 -save ref.fa KOBB0909_190_hong.fastq

1. Recevie the KOBB0909_190.sam file, I convert SAM to BAM

2. Run SAMTOOLS

samtools flagstat KOBB0909_190.bam

188214 in total

0 QC failure

0 duplicates

188214 mapped (100.00%)

0 paired in sequencing

0 read1

0 read2

0 properly paired (nan%)

0 with itself and mate mapped

0 singletons (nan%)

0 with mate mapped to a different chr

0 with mate mapped to a different chr (mapQ>=5)