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Summary.qual

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The summary.qual command reads a quality file and an optional name, and summarizes the quality information.


Default settings

You must provide a quality file.

mothur > summary.qual(qfile=summary.qual(qfile=stool.trim.pick.qual)

This command will produce a stool.trim.pick.qual.summary, which should look like:

Position	numSeqs	AverageQ	q0	q1	q2	...	q38	q39	q40	
0	1382	27.972504	0	0	0	0	...	11	0	4
1	1382	28.861795	0	0	0	0	...	27	0	7
2	1382	29.931982	0	0	0	0	...	28	0	21
3	1382	30.389292	0	0	0	0	...	32	0	21
4	1382	31.139652	0	0	0	0	...	53	0	23
5	1382	31.574530	0	0	0	0	...	66	0	33
6	1382	32.063675	0	0	0	0	...	85	0	45
7	1382	32.369755	0	0	0	0	...	97	0	47
8	1382	32.812592	0	0	0	0	...	110	0	75
9	1382	32.984081	0	0	0	0	...	132	0	68
...

Position - spot in sequence.
numSeqs - the number of sequence that had that position.
AverageQ - the average quality score
q0 - the number of sequence with a quality score of 0.
q1 - the number of sequence with a quality score of 1.
q2 - the number of sequence with a quality score of 2.
q3 - the number of sequence with a quality score of 3.
q4 - the number of sequence with a quality score of 4.
q5 - the number of sequence with a quality score of 5.
...
...
q40 - the number of sequence with a quality score of 40.

name

The name parameter allows you add a names file with your quality file.

mothur > summary.qual(qfile=stool.trim.pick.qual, name=stool.trim.unique.good.filter.names)


The screen output looks like:

Position	NumSeqs	AverageQ
0	2382	27.678001
100	2382	36.780018
200	2040	37.163727

count

The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information.

mothur > summary.qual(qfile=stool.trim.pick.qual, count=stool.trim.unique.good.filter.count_table)

processors

The processors option enables you to accelerate the alignment by using multiple processors. Default processors=Autodetect number of available processors and use all available.


Revisions

  • 1.23.0 First Introduced.
  • 1.28.0 Added count option
  • 1.40.0 Rewrite of threaded code. Default processors=Autodetect number of available processors and use all available.