I am working on a sets of paired end reads, in first step I trimmed them using Trimmomatic with following command
java -jar trimmomatic-0.36.jar PE 10.10B_R1.gz 10.10B_R2.gz D1R1P.fastq D1R1U.fastq D1R2P.fastq D1R2U.fastq LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:50
There are 201720569 reads in each output files (D1R1P.fastq and D1R2P.fastq). Then I mapped outputted files to reference genome using Bowtie2
bowtie2 -x reference -1 D1R1P.fastq -2 D1R2P.fastq --un-conc unmapped -S D1.sam
output of Bowtie2 say me this:
98031099 reads; of these: 98031099 (100.00%) were paired; of these: 10497294 (10.71%) aligned concordantly 0 times 73271391 (74.74%) aligned concordantly exactly 1 time 14262414 (14.55%) aligned concordantly >1 times
98.16% overall alignment rate
Why all paired reads are not including in mapping process?