thank you for the reply.

https://kb.10xgenomics.com/hc/en-us/articles/115003646912 In this article they have mentioned this method, they have used "samtools flagstat"

samtools flagstat pbmc_1k_v3_possorted_genome_bam.bam
76920923 + 0 in total (QC-passed reads + QC-failed reads)
10319036 + 0 secondary
0 + 0 supplementary
24785461 + 0 duplicates
73840063 + 0 mapped (95.99% : N/A)

...

In this duplicated reads is more than secondary.

i have also run same for my sample :

samtools flagstat sample_alignments.bam
31616795 + 0 in total (QC-passed reads + QC-failed reads)
31616795 + 0 primary
0 + 0 secondary
0 + 0 supplementary
19909293 + 0 duplicates
19909293 + 0 primary duplicates
31596859 + 0 mapped (99.94% : N/A)
31596859 + 0 primary mapped (99.94% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

in my bam you can see duplicated reads is much more. Is this correct way to calculate and what does it means 19909293 reads are duplicated in 31596859 reads mapped?

Is this affect my downstream analysis?

Thank you!!!