Table 1. lociNGS parameters for the summary screen (Sum; Fig. 1a) and the individual screen (Ind; Fig. 1b).

Screena	Parameterb	Fromc	*d	Definition
Sum	Individual	Demo		The individual's name
Sum	Population	Demo		The individual's population of origin
Sum	numLoci	Align	*	The number of loci called for each individual
Sum	totalReads	Align		Total number of reads sequenced in each individual
Sum	usedReads	Align		Total number of reads used for calling loci in this individual
Sum	percentUsed	lociNGS		UsedReads/TotalReads
Ind	LocusName	Loci		The name of the locus
Ind	Length	Loci		Number of bases in the locus
Ind	SNPs	Loci		Number of polymorphic sites
Ind	Number_Inds	Loci		Number of individuals called for this locus
Ind	Coverage_This_Ind	Align	**	Coverage for this locus in this individual
Ind	Coverage_Total	Align	**	Total coverage across individuals for this locus
Ind	Coverage_Used	Align	**	Total coverage for all individuals used in final locus

^aWhich screen the data are displayed on, the summary or the locus screen.

^bColumn header displayed in program; see Figure 1.

^cWhich input file the data are derived from, demographic data (demo), SAM/BAM alignments (Align), multi-FASTA locus files (loci) or calculated by lociNGS.

^d* indicates this column's data serve as a button to pull up locus screen; **indicates this column's data serves as a button to print the corresponding reads to a multi-FASTA file.