QC failed due to FASTQ file corruption
- FASTQ file is not a valid vcf.gz archive,
- FASTQ info file contains error messages, or
- FASTQ file is incomplete, corrupted either during download from the sequencer or during the upload to the DNA Pipeline account.
Sample is oversequenced
FASTQ file contains more than 2x as many reads as expected based on the following formula:
2 * (expected_coverage = 160 * num_of_cells = 20,000 * num_of_amplicons) / expected_ratio = 1 * num_of_tubes
QC failed due to a high percentage of Ns at a position
The position max Ns in R1 or R2 contains more than 20 % Ns. “N” replaces ATGC when the software is unable to make a base call for a position.
Could not detect chemistry
Fixed part counts for V1 and V2 chemistries are insufficient to reliably determine the chemistry of the sample.
Read more about the error detection process.