Table 3.

Summary of napiergrass single nucleotide polymorphism (SNP) markers mapped on the combined linkage map using 9 different software pipelines.

Software	Number of SNPs called	Total SNPs used for map construction	No. of SNPs on map	Percentage of SNPs on the map (%)
FreeBayes	25,193	6	0	0.00
GATK	197,475	52	5	0.26
SAMtools	27,082	3,377	151	7.89
GBS-SNP-CROP	2,906	115	52	2.72
TASSEL	7,326	116	56	2.93
Stacks	4,920	447	257	13.43
GBS-SNP-CROP de-novo	4,521	96	51	2.67
Stacks de-novo	6,871	339	185	9.67
TASSEL de-novo UNEAK	10,799	2,523	1,156	60.43
Total	287,093	7,071	1,913