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

[balags1]

We face similar issues when comparing read counts from public data assemblies. The number of countable reads directly from the file vs what quast reports show as "# total reads" are not identical. For Illumina data, we can calculate and understand that the paired nature of input data isn't taken into account, but that still doesn't explain why read counts of the same raw data vary so much.

[balags1]

Here's a comparison from 12 samples we analyzed.

NCBI SRA output # reads Quast # reads reads written : 5,101,034 5106239 reads written : 6,054,396 6057690 reads written : 3,578,388 3579502 reads written : 3,004,772 3011147 reads written : 1,133,924 1173786 reads written : 23,372,520 23391254 reads written : 1,706,432 1711560 reads written : 1,199,028 1283124 reads written : 1,824,162 2068696 reads written : 9,160,700 9177607 reads written : 1,937,778 2446295 reads written : 1,033,722 1034632 reads written : 1,587,460 1590464 reads written : 1,191,014 1266523