Genome analysis of Salmonella strains isolated from imported frozen fish in Burkina Faso

Kagambèga, Assèta; Belem, Salifou; McMillan, Elizabeth A.; Hiott, Lari M.; Ramadan, Hazem; Soro, Daniel K.; Sharma, Poonam; Gupta, Sushim K.; Barro, Nicolas; Jackson, Charlene R.; Frye, Jonathan G.

doi:10.1186/s13213-021-01642-8

Annals of Microbiology

Table 1 Assembly statistics of Salmonella strains

From: Genome analysis of Salmonella strains isolated from imported frozen fish in Burkina Faso

Isolate ID	Contigs	Scaffolds	Genome size	Longest scaffold	N50	Raw reads	EC reads	% reads passing EC	Raw nt	EC nt	% nt passing EC	Raw cov	EC cov	Median cov	10th percentile cov	Bases ≥ Q40	% GC
87	61	61	4621725	703602	292745	2075760	2055651	99.03	3.9E+08	3.6E+08	93.77	83.55	78.35	82	59	4617943	52.2
88	61	61	4654102	433362	231906	2480308	2461694	99.25	3.5E+08	3.4E+08	97.2	74.39	72.31	73	54	4651947	52.2
89	180	180	5345366	265739	89976	1585778	1571781	99.12	2.1E+08	2E+08	96.96	39.18	37.99	37	24	5332372	51.8
95	40	40	4680005	668083	504361	2410566	2379641	98.72	4.7E+08	4.4E+08	92.32	100.7	93.01	97	72	4679387	52.2
98	63	63	4918496	775042	398010	1718264	1687773	98.23	3.3E+08	3.1E+08	92.42	67.53	62.41	65	46	4916559	51.9
100	80	80	4963160	748091	287769	2265232	2202986	97.25	4.4E+08	3.9E+08	88.29	89.07	78.65	85	62	4961107	52
101	52	52	4902134	944301	501799	1868462	1821376	97.48	3.8E+08	3.4E+08	90.4	77.46	70.02	74	54	4900597	51.8
103	49	49	4749239	1151741	340547	2323594	2296420	98.83	4.5E+08	4.2E+08	93.23	93.97	87.61	87	63	4748210	52.2
108	44	44	4738594	568197	405801	2091224	2069633	98.97	3.6E+08	3.5E+08	95.15	76.54	72.83	74	55	4737525	52.2
111	47	47	4741632	568232	454680	2514870	2487391	98.91	4.9E+08	4.5E+08	92.81	102.4	95.07	99	76	4740854	52.2
113	49	49	4749008	1444467	340548	2281594	2260595	99.08	4.6E+08	4.3E+08	93.21	97.31	90.7	92	69	4748045	52.2
116	38	38	4661074	871623	424548	1877226	1855294	98.83	3.6E+08	3.3E+08	92.87	76.86	71.37	74	54	4659622	52.2
117	44	44	4739093	568232	427385	2101626	2085634	99.24	3.6E+08	3.5E+08	95.73	76.7	73.42	74	55	4738049	52.2
119	51	51	4730026	508935	323835	1916062	1891245	98.7	2.5E+08	2.4E+08	97.36	52	50.62	50	35	4728141	52.2
122	64	64	4732251	461578	226770	2578950	2550077	98.88	3.4E+08	3.3E+08	96.81	72.58	70.26	71	49	4730117	52.2
127	46	46	4740433	568232	394001	1464044	1447638	98.88	2.6E+08	2.4E+08	95.1	53.95	51.31	52	36	4738090	52.2
128	52	52	4729542	454349	323835	1476660	1454883	98.53	1.9E+08	1.8E+08	97.27	39.56	38.48	38	26	4726471	52.2
129	43	43	4617569	720868	300407	1313142	1295563	98.66	2.4E+08	2.2E+08	93.89	51.58	48.43	50	34	4614768	52.2
130	43	43	4740056	568232	400228	3575342	3520930	98.48	6.6E+08	6E+08	91.2	138.7	126.5	133	101	4739679	52.2
131	53	53	4741832	568232	394156	1566306	1545820	98.69	2.9E+08	2.7E+08	91.49	62.2	56.91	60	42	4739118	52.2
134	34	34	4797111	1850190	750647	2710124	2671347	98.57	5.3E+08	4.8E+08	91.32	110.4	100.8	106	78	4796675	52.2
135	54	54	4903282	944125	424401	2061468	1996430	96.85	3.7E+08	3.3E+08	87.78	75.59	66.35	71	50	4901400	51.8
136	46	46	4747148	857353	340487	1895802	1849828	97.57	3.3E+08	3E+08	90	69.25	62.33	63	43	4745627	52.2
137	44	44	4739464	514012	394016	2219520	2160947	97.36	4.1E+08	3.6E+08	88.01	87.08	76.64	83	60	4738438	52.2
138	42	42	4617148	720868	331382	1581084	1563497	98.89	3.1E+08	2.8E+08	90.95	67.5	61.39	65	46	4615739	52.2
139	45	45	4740410	514012	394637	2120290	2100494	99.07	3.8E+08	3.6E+08	94.39	80.57	76.06	78	56	4739354	52.2
141	71	71	4730418	434837	164778	1976130	1952830	98.82	2.7E+08	2.6E+08	96.44	56.5	54.49	55	39	4726407	52.2
142	45	45	4620013	720868	387756	2282854	2264502	99.2	4.4E+08	4.1E+08	93.92	95.63	89.81	93	68	4619149	52.2
144	688	688	5699254	126378	26527	1655604	1640692	99.1	3.3E+08	3.1E+08	93.14	58.29	54.29	58	27	5652021	51.6
146	385	385	5031347	222688	74906	2781576	2757394	99.13	3.7E+08	3.6E+08	97.48	72.79	70.96	73	46	4988376	52.1

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