Total reads

The total number of reads in all fastq files

Barcoded reads

Number of reads with barcodes written by the bxcheck trim command

Bad reads

Reads excluded for various reasons (low mapping quality, flag, mate mapped to a different chromosome)

Reads in good fragments

Number of good reads in good fragments

N50

Shortest fragment at 50% of the total length: sort fragments by their size in ascending order, mark the center of the entire length and report the size of the fragment which happens to be in the middle.

N10x

Longest fragment at 10x genome coverage: sort fragments by their size in descending order, mark the point where the distance from the beginning divided by the genome length is at least 10 and report the size of the fragment which happens to be at that point. Note that the genome length is determined from the BAM header as the sum of all contigs.

Cumulative fraction of pairs / Reads pairs per fragment

Cumulative frequency of read pairs in fragments with this many read pairs per fragment. The data was truncated to include at least 95.0% of read pairs.

Number of fragments (density) / Fragment length

Fragment size distribution plotted as density. The fragment size is calculated as D + D/(N-1), where N is the number of read pairs within the fragment and D is the distance between the first and the last pair. All read pairs must map to the same chromosome with the maximum gap of 100,000 bp. Only fragments with more than 2 read pairs are included.

Sequenced bases / Fragment length

Total number of sequence in fragments of given length.

Fragment length / Nx coverage

Like N10x above, but calculated for all depths.