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

Table 1

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

Sample	Number of raw reads	Number of clean reads	Number of assembled contigs	Number of observed OTUs
CN1	739,235	727,578	1,210	35
CN2	721,871	709,914	6,181	12
CN3	1,316,673	1,294,994	5,314
CN4	962,476	946,762	1,312	11
CN5	1,183,395	1,164,692	3,553	23
CN6	972,083	954,980	3,704	31
DK1	1,083,848	1,064,236	2,268	27
DK2	1,866,041	1,836,634	5,244	32
DK3	1,381,344	1,064,236	11,450
DK4	1,254,999	1,235,172	3,004	23
GF1	1,078,026	1,060,498	4,361	43
GS1	1,181,800	1,163,704	4,220	18
GS2	1,366,750	1,345,650	7,775	23
PN2	243,351	239,606	406	20
PN3	183,080	179,774	236	3
TY1	1,467,223	1,443,986	5,852	17
Total	17,002,195	16,432,416	66,090	301