FastQC Metrics Output

The FastQC metrics are output to a CSV file format in the run output directory called <PREFIX>.fastqc_metrics.csv.

The reported metrics are broken down into eight sections by metric type. Each section is broken down further into separate rows by either the length, position, or other relevant categorical variables. The following are the metric sections.

•

Read Mean Quality—Total number of reads. Each average Phred-scale quality value is rounded to the nearest integer.

•

Positional Base Mean Quality—Average Phred-scale quality value of bases with a specific nucleotide and at a given location in the read. Locations are listed first and can be either specific positions or ranges. The nucleotide is listed second and can be A, C, G, or T. N or ambiguous bases are assumed to have the system default value, usually QV2.

•

Positional Base Content—Number of bases of each specific nucleotide at given locations in the read. Locations are given first and can be either specific positions or ranges. The nucleotide is listed second and can be A, C, G, T, N.

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Read Lengths— Total number of reads with each observed length. Lengths can be either specific sizes or ranges, depending on the settings specified using --fastqc-granularity.

•

Read GC Content—Total number of reads with each GC content percentile between 0 % and 100 %.

•

Read GC Content Quality—Average Phred-scale read mean quality for reads with each GC content percentile between 0% and 100%.

•

Sequence Positions—Number of times an adapter or other kmer sequence is found, starting at a given position in the input reads. Sequences are listed first in the metric description in quotes. Locations are listed second and can be either specific positions or ranges.

•

Positional Quality—Phred-scale quality value for bases at a given location and a given quantile of the distribution. Locations are listed first and can be either specific positions or ranges. Quantiles are listed second and can be any whole integer 0–100.

The following are examples rows from each section.

Section	Mate	Metric	Value
READ MEAN QUALITY	Read1	Q38 Reads	965377
...
POSITIONAL BASE MEAN QUALITY	Read1	ReadPos 145-152 T Average Quality	34.49
POSITIONAL BASE MEAN QUALITY	Read1	ReadPos 150 T Average Quality	34.44
POSITIONAL BASE MEAN QUALITY	Read1	ReadPos 256+ T Average Quality	36.99
...
POSITIONAL BASE CONTENT	Read1	ReadPos 145-152 A Bases	113362306
POSITIONAL BASE CONTENT	Read1	ReadPos 150 A Bases	14300589
POSITIONAL BASE CONTENT	Read1	ReadPos 256+ A Bases	13249068
...
READ LENGTHS	Read1	150bp Length Reads	77304421
READ LENGTHS	Read1	144-151bp Length Reads	77304421
READ LENGTHS	Read1	>=255bp Length Reads	1000000
...
READ GC CONTENT	Read1	50% GC Reads	140878674373
...
READ GC CONTENT QUALITY	Read1	50% GC Reads Average Quality	36.20
...
SEQUENCE POSITIONS	Read1	'AGATCGGAAGAG' 137bp Starts	20
SEQUENCE POSITIONS	Read1	'AGATCGGAAGAG' 137-144bp Starts	23
...
POSITIONAL QUALITY	Read1	ReadPos 150 50% Quantile QV	37
POSITIONAL QUALITY	Read1	ReadPos 145-152 50% Quantile QV	37
...