mapped reads count in reads_report

[QianGuoPKU]

Hi,

I am reaching out for your help on the intepretation of the reads_report.

In my result, the raw data fastq included 26,362,661 reads in total. However, "#Assembly mapped" and "#Reference mapped" were reported as 42,433,073 and 31,999,068, respectively, both were more than the reads number (> 26,362,661). How to interpret the "#Assembly mapped" and "#Reference mapped"? Do they mean the count of mapped reads or the count of hits in the alignment, or anything else?

And I'd also like to ask for your help on interpreting the transposed_report. I am wondering which columns can convey the information on the misassemblies caused by transposable elements (TE)? In my file, I couldn't find any information of TE-related misassemblies or mismatches.

Please find the reads_report and transposed_report enclosed.

Any information and insights into the above questions would be much appreciated!

Best,
Zoe

reads_report.txt
transposed_report.txt