Interpreting read_count_table Numbers?

Hello, I am running kneaddata (v0.10.0) through biobakery workflows on paired reads, but I have not been able to find a description of how to interpret the read_count_table output.

Below are the counts for R1:
|raw pair1|21281592|
|trimmed pair1|17048604|
|trimmed orphan1|529656|
|decontaminated hg37dec_v0.1 pair1|10060306|
|decontaminated hg37dec_v0.1 orphan1|744693|
|final pair1|10060306|
|final orphan1|744693|

And here for R2:
|raw pair2|21281592|
|trimmed pair2|17048604|
|trimmed orphan2|329832|
|decontaminated hg37dec_v0.1 pair2|10060306|
|decontaminated hg37dec_v0.1 orphan2|1246013|
|final pair2|10060306|
|final orphan2|1246013|


  1. What does each of these numbers mean? I have some guesses, but would love an “official” description.
  2. How should I calculate the % human reads removed?
  3. Are there any default qc thresholds in kneaddata/biobakery, or any suggested ones?

Thank you in advance!