BWA-meth mapping issues

[alirazzaq254]

Hi,
I am using bwa-meth to map paired-end reads and getting the following results
633899747 + 365387445 in total (QC-passed reads + QC-failed reads)
573478916 + 264212420 primary
60420831 + 101175025 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
633127309 + 365293487 mapped (99.88% : 99.97%)
572706478 + 264118462 primary mapped (99.87% : 99.96%)
573478916 + 264212420 paired in sequencing
286739458 + 132106210 read1
286739458 + 132106210 read2
286779006 + 0 properly paired (50.01% : 0.00%)
572222622 + 264024504 with itself and mate mapped
483856 + 93958 singletons (0.08% : 0.04%)
78101526 + 51005926 with mate mapped to a different chr
10620402 + 6909652 with mate mapped to a different chr (mapQ>=5)

Could you please help me with how can avoid the quality failed reads and how I can improve the paired reads mapping rate.
I used both R1 and R2 without trimming.