The seasonal changes of the gut microbiome of the population living in traditional lifestyles are represented by characteristic species-level and functional-level SNP enrichment patterns

Table 1 Comparison of the SNP identification results by the three tools. In these simulated data, the SNP coverages (defined as the number of SNPs identified by the software on these five genomes, divided by the sum of the five genome sizes) were also shown for different tools and different sequencing depths

Tool	Depth	Match	# False positive	# False negative	# All SNPs	SNP Coverage (%)	Sensitivity (%)	Selectivity (%)
GATK	5x	10,567	52	218	10,619	0.078	98.0	99.5
VarScan2	5x	10,283	0	502	10,283	0.076	95.3	100.0
BCFtools	5x	10,635	24	150	10,659	0.078	98.6	99.8
GATK	10x	10,590	6	195	10,596	0.076	98.2	99.9
VarScan2	10x	10,647	0	138	10,647	0.078	98.7	100.0
BCFtools	10x	10,656	0	129	10,656	0.078	98.8	100.0
GATK	20x	10,599	0	186	10,599	0.078	98.3	1.000
VarScan2	20x	10,661	0	124	10,661	0.078	98.9	100.0
BCFtools	20x	10,663	0	122	10,663	0.078	98.9	100.0
GATK	40x	10,607	0	178	10,607	0.078	98.3	100.0
VarScan2	40x	10,667	0	118	10,667	0.078	98.9	100.0
BCFtools	40x	10,665	0	120	10,665	0.078	98.9	100.0

ISSN: 1471-2164