Metagenomic Characterization of Poultry Cloacal and Oropharyngeal Swabs in Kenya Reveals Bacterial Pathogens and Their Antimicrobial Resistance Genes

Table 2

Number of raw reads, clean reads, assembled contigs, and observed number of OTUs identified in oropharyngeal swab samples.

Sample	Number of raw reads	Number of clean reads	Number of assembled contigs	Number of observed OTUs
CN7	1,508,846	1,486,620	9,637	14
CN8	270,122	265,624	881	40
CN9	574,055	565,378	3,586	28
CN10	2,382,576	2,348,126	13,704
CN12	1,570,585	1,545,050	6,892	11
DK5	1,097,134	1,080,036	13,472	38
DK6	562,109	552,610	4,997	14
GF2	413,234	406,648	990	20
GS3	807,239	793,946	2,657	29
GS4	429,261	422,556	722	47
PN4	320,162	315,052	479	5
PN5	437,675	431,732	719	7
PN6	268,587	264,240	372	4
TY2	408,787	402,166	990	18
Total	11,050,372	10,879,784	60,098	275