Table 8.

Parameters in LifeScope’s secondary and tertiary analysis software modules

	Default value
Alignment parameters
Minimum number of non-matches allowed during indel finding	9
Maximum deletion size (in a gapped alignment in the first pass)	19
Maximum insertion size (in a gapped alignment in the first pass)	4
The minimum edge length required for insertions and deletions on the first pass	12
Number of mismatches allowed for gap alignments	3
Minimum mapping quality value (MAPQ) allowed for aligned read	8
Minimum edge length required for insertions and deletions	12
The seed window side allowed to the left of the anchor alignment	40
The seed window side allowed to the right of the anchor alignment	80
Maximum number of alignments for a read on the first pass which gives the maximum number of hits that are reported in the mapping output	50
SNPs analysis module using diBayes algorithm variant calling parameters
Minimum allele ratio (Het)	0.15
Minimum coverage (Het)	2
Minimum non-reference base QV (Het)	28
Minimum average non-reference base QV (Hom)	28
Minimum base quality value for a position	28
Minimum base quality value of the non-reference allele of a position	28
Mapping quality value of the read	$>$8
SNP call stringency. Alleles on both strands	Not required
Threshold of mismatch/alignment-lengh ratio	1
Base candidate allele quality value	$>$7
Minimum number of unique start positions required to call heterozygote, homozygote	2
Proportion of the total reads containing either of the two candidate alleles	0.65