I ask a question about term "downstream".
I know that downstream refers to the direction of 3'. That is all I have learned.
While reading below sentence, however, I am so confused that why the term "downstream" was used.
"After mapping reads to the reference genome, a three step post-alignment processing procedure is recommended to minimize the artifacts that may affect the quality of downstream variant calling. It consists of read duplicate removal, indel realignment, and base quality score recalibration.
"Base quality is a critical factor for accurate variant detection in the downstream analysis."
I fully understood above sentence except the downstream.
I cannot connect downstream I knew with the potential meaning in the sentence.
Could you help me why the term downstream was used for those sentence?