UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study

Table 2 Summary statistics obtained for each of the three enzyme combinations for a subset of 1 M reads

Enzyme combination	Accession	Total read number	Number of stacks (tags) within samples^a	Number of stacks (tags) common to all samples^b	Number of polymorphic tags^c	Number of polymorphic SNPs^c	Average depth of scored SNPs
PstI/MspI	KNE 796	5,720,433	83,082	22,191			15.20
	MD-20	5,418,738	64,382		4440	4515	15.64
	Okhale-1	7,738,023	73,903				17.21
PstI/MspI + ApeKI	KNE 796	3,466,582	50,189	12,249			16.57
	MD-20	4,474,070	37,619		2475	2509	20.90
	Okhale-1	5,586,989	45,829				19.65
PstI/NdeI	KNE 796	6,647,185	39,406	12,392			32.28
	MD-20	4,269,463	35,218		3232	3305	28.66
	Okhale-1	5,851,494	37,551				34.76

^aDetermined using ‘ustacks’
^bGBS tags that are common to all three accessions were selected from the ‘ASustacks’ output; if two or more tags had a level of homology ≥98%, only a single tag was retained
^cOnly SNPs at a read depth ≥ 8× were scored

ISSN: 1471-2229