MAQ Gene

General Settings

/	Results directory and file prefix. (letters, numbers, underscore, hyphen)
	Reference Genome
	Ignore cache and rerun everything.
	Make extra MAQ analysis files (.cq .view .aref)
	Minimum span of uncovered bases to report as uncovered region

Choose Lanes from Flow Cell(s)

Set parameters for mapping, assembly and pileup

Description	map	assemble	pileup
maximum number of mismatches in first 28 bases
maximum sum of error qualities
length of first read to use (<127) (0 to use full read length)
length of the second read to use (<127) (0 to use full read length)
rate of difference between reads and references
adapter sequence (3-base barcode for this sample)
max distance between two paired reads
max distance between two RF paired reads
max number of hits to output. >512 for all 01 hits.
disable Smith-Waterman alignment for non-mapping 2nd-mate
maximum number of mismatches over entire read
number of haplotypes (>=2) [2]
expected rate of heterozygotes
use worst single-end mapping quality as quality for both mates
discard abnormal pairs
minimum mapping quality

Define a Point Mutation as...

Consensus quality score ≥		Neighborhood quality ≥
Non-wildtype reads ≥		Loci multiplicity ≤
Total sequencing depth ≥		Fraction non-wildtype reads ≥

Mutation-to-gene association

Number of intervening exons ≤
Maximum distance (bp) from gene start:	directly neighboring mutation	indirectly neighboring mutation
Maximum distance (bp) from gene end:	directly neighboring mutation	indirectly neighboring mutation