# For each of the modules you can choose to not run that
# module at all by setting the value below to 1 for the
# modules you want to remove.
duplication 		ignore 		0
kmer 				ignore 		0
n_content 			ignore 		0
overrepresented 	ignore 		0
quality_base 		ignore 		0
sequence 			ignore 		0
gc_sequence			ignore 		0
quality_sequence	ignore		0
tile				ignore		0
sequence_length		ignore		0
adapter				ignore		0

# For the duplication module the value is the percentage
# remaining after deduplication.  Measured levels below
# these limits trigger the warning / error.
duplication	warn	70
duplication error	50

# For the kmer module the filter is on the -log10 binomial
# pvalue for the most significant Kmer, so 5 would be 
# 10^-5 = p<0.00001
kmer	warn	2
kmer	error	5

# For the N module the filter is on the percentage of Ns
# at any position in the library
n_content	warn	2
n_content	error	10

# For the overrepresented seqs the warn value sets the
# threshold for the overrepresented sequences to be reported
# at all as the proportion of the library which must be seen
# as a single sequence
overrepresented	warn	0.1
overrepresented	error	1

# The per base quality filter uses two values, one for the value
# of the lower quartile, and the other for the value of the
# median quality.  Failing either of these will trigger the alert
quality_base_lower	warn	10
quality_base_lower	error	5
quality_base_median	warn	25
quality_base_median	error	20

# The per base sequence content module tests the maximum deviation
# between A and T or C and G
sequence	warn	10
sequence	error	20

# The per sequence GC content tests the maximum deviation between
# the theoretical distribution and the real distribution
gc_sequence	warn	15
gc_sequence	error	30

# The per sequence quality module tests the phred score which is
# most frequently observed
quality_sequence	warn	27
quality_sequence	error	20

# The per tile module tests the maximum phred score loss between 
# and individual tile and the average for that base across all tiles
tile	warn	5
tile	error	10

# The sequence length module tests are binary, so the values here
# simply turn them on or off.  The actual tests warn if you have
# sequences of different length, and error if you have sequences
# of zero length.

sequence_length	warn	1
sequence_length	error	1

# The adapter module's warnings and errors are based on the 
# percentage of reads in the library which have been observed
# to contain an adapter associated Kmer at any point

adapter	warn	2
adapter	error	5


	