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author jjjjia
date Tue, 14 Aug 2018 17:18:49 -0400
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2018-08-10 20:59:10.151624

ID: ASDF
Assembly: ASDF



~~~~~~~MLST summary~~~~~~~
MLST determined species: Klebsiella pneumoniae

MLST Details: 
/home/jjjjia/testCases/cpoResults/contigs/BC11-Kpn005_S2.fa	kpneumoniae	147	gapA(3)	infB(4)	mdh(6)	pgi(1)	phoE(7)	rpoB(4)	tonB(38)

MLST information: 
!!!MLST determined species is NOT the same as expected species, contamination? mislabeling?



~~~~~~~~Plasmids~~~~~~~~

predicted plasmid origins: 
;IncFIB;IncFII;ColRNAI_rep_cluster_1987;rep_cluster_1195;ColRNAI_rep_cluster_1987,rep_cluster_2050

definitely plasmid contigs
00031;00019;00025;00035;00038;00039

likely plasmid contigs
00054;00033;00061;00062;00040;00063;00021;00050;00027;00052;00032;00045;00048;00047;00060;00049;00064;00029;00036;00028

mob-suite prediction details: 
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00054_len=1680_cov=99.4_corr=0_spades=NODE_54_length_1680_cov_99.397296_pilon	1680	Incomplete					KY271404	0.0163307	KU736877	IS3	3097.0	9280.0	10959.0
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00033_len=7099_cov=71.4_corr=0_spades=NODE_33_length_7099_cov_71.391566_pilon	7099	Incomplete					KY271404	0.0163307					
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00061_len=1290_cov=63.7_corr=0_spades=NODE_61_length_1290_cov_63.717111_pilon	1290	Incomplete					KY271404	0.0163307	CP001182	IS6	1733.0	45808.0	46813.0
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00062_len=1261_cov=94.7_corr=0_spades=NODE_62_length_1261_cov_94.707231_pilon	1261	Incomplete					KY271404	0.0163307	EU327987	IS91	1790.0	1.0	1167.0
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00040_len=4267_cov=45.7_corr=0_spades=NODE_40_length_4267_cov_45.722222_pilon	4267	Incomplete					KY271404	0.0163307	MF168946	IS3	1055.0	57274.0	58321.0
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00063_len=1231_cov=111.8_corr=0_spades=NODE_63_length_1231_cov_111.776268_pilon	1231	Incomplete					KY271404	0.0163307	MG764534	Tn3	1792.0	123.0	1353.0
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00021_len=50545_cov=56.2_corr=0_spades=NODE_21_length_50545_cov_56.199215_pilon	50545	Incomplete					KY271404	0.0163307					
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00050_len=2206_cov=232.0_corr=0_spades=NODE_50_length_2206_cov_232.019240_pilon	2206	Incomplete					KY271404	0.0163307	MF344564	ISNCY	4047.0	26.0	2231.0
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00027_len=23176_cov=57.2_corr=1_spades=NODE_27_length_23176_cov_57.154584_pilon	23176	Incomplete					KY271404	0.0163307					
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00052_len=1916_cov=74.5_corr=0_spades=NODE_52_length_1916_cov_74.495808_pilon	1916	Incomplete					KY271404	0.0163307					
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00031_len=9290_cov=61.3_corr=0_spades=NODE_31_length_9290_cov_61.312889_pilon	9290	Incomplete	IncFIB	000107__CP014778_00094			KY271404	0.0163307					
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00032_len=8550_cov=90.1_corr=0_spades=NODE_32_length_8550_cov_90.057224_pilon	8550	Incomplete					KY271404	0.0163307					
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00045_len=2914_cov=67.7_corr=0_spades=NODE_45_length_2914_cov_67.672049_pilon	2914	Incomplete					KY271404	0.0163307	EU780013	IS5	1230.0	22192.0	23343.0
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00048_len=2286_cov=54.9_corr=0_spades=NODE_48_length_2286_cov_54.938861_pilon	2286	Incomplete					KY271404	0.0163307					
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00047_len=2438_cov=67.3_corr=0_spades=NODE_47_length_2438_cov_67.279100_pilon	2438	Incomplete					KY271404	0.0163307	KF306092	IS30	2737.0	3022.0	4503.0
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00060_len=1334_cov=206.0_corr=0_spades=NODE_60_length_1334_cov_205.993372_pilon	1334	Incomplete					KY271404	0.0163307	KX710093	Tn3	1941.0	21.0	1353.0
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00049_len=2226_cov=74.2_corr=0_spades=NODE_49_length_2226_cov_74.201048_pilon	2226	Incomplete					KY271404	0.0163307					
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00019_len=68857_cov=55.7_corr=0_spades=NODE_19_length_68857_cov_55.651782_pilon	68857	Incomplete	IncFII	000132__HG969996,000113__CP022035	MOBF	NC_021231_00058	KY271404	0.0163307					
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00064_len=1218_cov=229.8_corr=0_spades=NODE_64_length_1218_cov_229.791017_pilon	1218	Incomplete					KY271404	0.0163307	MF344562	IS3	2250.0	381.0	1598.0
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00025_len=33717_cov=69.1_corr=0_spades=NODE_25_length_33717_cov_69.149628_pilon	33717	Incomplete	IncFIB	000097__NC_025166_00051			KY271404	0.0163307					
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00029_len=19880_cov=51.1_corr=0_spades=NODE_29_length_19880_cov_51.127221_pilon	19880	Incomplete					KY271404	0.0163307					
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00036_len=5070_cov=128.9_corr=0_spades=NODE_36_length_5070_cov_128.854744_pilon	5070	Incomplete					KY271404	0.0163307					
BC11-Kpn005_S2.fa	770	BC11-Kpn005_S2.fa|contig00028_len=20810_cov=52.4_corr=0_spades=NODE_28_length_20810_cov_52.435285_pilon	20810	Incomplete					KY271404	0.0163307					
BC11-Kpn005_S2.fa	190	BC11-Kpn005_S2.fa|contig00035_len=5334_cov=187.2_corr=0_spades=NODE_35_length_5334_cov_187.195698_pilon	5334	Incomplete	ColRNAI_rep_cluster_1987	000019__CP000651_00005	MOBP	NC_019986_00002,NC_001848_00006	CP018444	0.00038558099999999997					
BC11-Kpn005_S2.fa	2088	BC11-Kpn005_S2.fa|contig00038_len=4444_cov=185.7_corr=0_spades=NODE_38_length_4444_cov_185.662497_pilon	4444	Incomplete	rep_cluster_1195	000483__CP010949_00006			KY454616	0.00985499					
BC11-Kpn005_S2.fa	novel_0	BC11-Kpn005_S2.fa|contig00039_len=4290_cov=125.7_corr=0_spades=NODE_39_length_4290_cov_125.717752_pilon	4290	Incomplete	ColRNAI_rep_cluster_1987,rep_cluster_2050	000019__CP000651_00005,001473__CP024541			CP018739	0.061583900000000004					



~~~~~~~~AMR Genes~~~~~~~~

predicted carbapenamase Genes: 
OXA-181(plasmid)
other RGI AMR Genes: 

Details about the carbapenamase Genes: 
/home/jjjjia/testCases/cpoResults/contigs/BC11-Kpn005_S2.fa	contig00038	256	1053	OXA-181	1-798/798	===============	0/0	100.0	100.0	bccdc	AEP16366.1	  OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-181 

Details about the RGI AMR Genes: