Interpreting ATAC-seq alignment results

Question

[hara]

I have two ATAC-seq data samples which I aligned to reference genome hg19 using STAR aligner. How do I judge the quality of the data? I am new to ATAC-sequencing and understanding the data quality. The mapping results are as below: **

• Sample 1:

* Tags mapped %: 22.32 Multi-mapped reads %: 1.23 Mapped duplicates %: 5.44 Tags unmapped %: 71.01 *

• Sample 2:

** Tags mapped %: 41.80 Multi-mapped reads %: 2.90 Mapped duplicates %: 13.43 Tags unmapped %: 41.88

[ATpoint]

Does your reference genome contain chrM? Based on the unmapped percentage, I bet it doesn't. Are these primary samples or cell lines and what protocol has been used to generate them?