samtools flagstat Aligned.out.sorted.bam > flagstat.txt

Mapping evaluation results

14836 + 0 in total (QC-passed reads + QC-failed reads)
936 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
14836 + 0 mapped (100.00% : N/A)
13900 + 0 paired in sequencing
6950 + 0 read1
6950 + 0 read2
13900 + 0 properly paired (100.00% : N/A)
13900 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)