Table 1.

Quality and characteristics of sequences from cesarean-derived conventional (CV; n = 4) and germ-free (GF; n = 4) piglets from the same litter.

Piglets	Tissue	Raw reads	Clean reads	Clean bases	Clean reads (%)	Error rate (%)	Q20 (%)	Q30 (%)	GC content (%)
GF	Jejunum	48288268	43596668	6.54 G	90.28%	0.02	95.69	90.23	51.30
	Colon	62040000	56094262	8.41 G	90.42%	0.02	95.80	90.44	50.94
	Spleen	46332068	41867278	6.28 G	90.36%	0.02	95.67	90.18	51.68
	Liver	52371044	47750376	7.16 G	91.18%	0.02	95.73	90.13	50.32
	Oral mucosa	52206896	47073820	7.06 G	90.17%	0.02	95.24	89.32	52.38
CV	Jejunum	50648344	43996026	6.6 G	86.87%	0.02	94.64	88.27	51.41
	Colon	49030906	44001630	6.6 G	89.74%	0.02	95.50	89.80	51.22
	Spleen	51290870	47306252	7.1 G	92.23%	0.02	95.59	89.91	52.02
	Liver	56142822	49496190	7.42 G	88.16%	0.02	95.16	89.16	51.40
	Oral mucosa	54799658	51563930	7.73 G	94.10%	0.02	95.87	90.51	52.16

Q20 and Q30 represent the proportion of bases with Phred quality scores >20 and >30, respectively.