samtool fixmate drastically decreases the number of properly paired reads

[Jerry-cs]

After samtools namesort + fixmate, the number of properly paired reads decreases from 35.42% to 8%.

Does anyone know the reason?

Before namesort and fixmate
800000 in total
0 QC failure
0 duplicates
331347 mapped (41.42%)
800000 paired in sequencing
400000 read1
400000 read2
283386 properly paired (35.42%)
287049 with itself and mate mapped
44298 singletons (5.54%)
3314 with mate mapped to a different chr
1491 with mate mapped to a different chr (mapQ>=5)


After namesort and fixmate

800000 in total
0 QC failure
0 duplicates
331347 mapped (41.42%)
800000 paired in sequencing
400000 read1
400000 read2
64026 properly paired (8.00%)
64856 with itself and mate mapped
266491 singletons (33.31%)
744 with mate mapped to a different chr
321 with mate mapped to a different chr (mapQ>=5)

[epigen]

Have you found out what went wrong?
It seems the pairs were matched correctly because the number of singletons increased drastically:
before:
287049 with itself and mate mapped
44298 singletons (5.54%)

after:
64856 with itself and mate mapped
266491 singletons (33.31%)