Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

Quick, Joshua; Ashton, Philip; Calus, Szymon; Chatt, Carole; Gossain, Savita; Hawker, Jeremy; Nair, Satheesh; Neal, Keith; Nye, Kathy; Peters, Tansy; De Pinna, Elizabeth; Robinson, Esther; Struthers, Keith; Webber, Mark; Catto, Andrew; Dallman, Timothy J.; Hawkey, Peter; Loman, Nicholas J.

doi:10.1186/s13059-015-0677-2

Table 1 Streaming alignment statistics from nanopore data

From: Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

Flowcell	Time (m)	Reads	Bases	Positions	Missing bases	Covered (%)	True positive	True negative	False positive	False negative	Recall	Precision	Accuracy
Outbreak	60	920	5635627	7091	6463	8.86	10	617	0	2	0.83	1.00	0.09
Outbreak	120	2037	12853716	7091	4815	32.10	26	2237	7	7	0.79	0.79	0.32
Outbreak	180	3040	19297035	7091	3580	49.51	48	3436	13	15	0.76	0.79	0.49
Outbreak	240	3933	24900526	7091	2703	61.88	62	4291	17	19	0.77	0.78	0.61
Outbreak	300	4525	28614437	7091	2236	68.47	70	4736	25	25	0.74	0.74	0.68
Outbreak	360	5654	35848389	7091	1499	78.86	82	5454	26	31	0.73	0.76	0.78
Outbreak	420	6680	42498530	7091	1029	85.49	87	5914	25	37	0.70	0.78	0.85
Outbreak	480	7516	47950926	7091	749	89.44	94	6185	30	34	0.73	0.76	0.89
Outbreak	540	7913	50372188	7091	630	91.12	96	6300	29	37	0.72	0.77	0.90
Outbreak	600	8807	56254898	7091	463	93.47	103	6470	20	36	0.74	0.84	0.93
Outbreak	660	9666	61989423	7091	337	95.25	107	6588	22	38	0.74	0.83	0.94
Outbreak	720	10472	67171497	7091	267	96.23	111	6659	16	39	0.74	0.87	0.95
Outbreak	780	10833	69363106	7091	243	96.57	112	6686	16	35	0.76	0.88	0.96
Outbreak	840	11708	74625788	7091	191	97.31	117	6737	13	34	0.77	0.90	0.97
Outbreak	900	12479	79551399	7091	141	98.01	121	6780	16	34	0.78	0.88	0.97
Outbreak	960	13198	84228957	7091	120	98.31	124	6797	16	35	0.78	0.89	0.98
Outbreak	1020	13579	86600020	7091	107	98.49	125	6808	16	36	0.78	0.89	0.98
Outbreak	1080	14359	91437571	7091	90	98.73	126	6823	17	36	0.78	0.88	0.98
Outbreak	1140	15168	96646434	7091	74	98.96	124	6842	15	37	0.77	0.89	0.98
Outbreak	1200	15835	100970757	7091	70	99.01	123	6851	12	36	0.77	0.91	0.98
Outbreak	1260	16205	103367082	7091	63	99.11	124	6857	11	37	0.77	0.92	0.98
Outbreak	1320	16632	106040214	7091	60	99.15	125	6859	12	36	0.78	0.91	0.98
Outbreak	1380	17184	109618605	7091	56	99.21	125	6863	11	37	0.77	0.92	0.99
Outbreak	1440	17332	110500445	7091	55	99.22	124	6865	11	37	0.77	0.92	0.99
Non-outbreak	60	1268	5382184	7091	6372	10.14	1	717	2	0	1.00	0.33	0.10
Non-outbreak	120	2554	11567191	7091	4791	32.44	2	2284	15	0	1.00	0.12	0.32
Non-outbreak	180	3626	17058822	7091	3451	51.33	4	3607	29	1	0.80	0.12	0.51
Non-outbreak	240	4612	22004574	7091	2500	64.74	11	4545	32	4	0.73	0.26	0.64
Non-outbreak	300	5483	26582592	7091	1760	75.18	13	5281	35	3	0.81	0.27	0.75
Non-outbreak	360	6198	30340527	7091	1330	81.24	15	5705	40	2	0.88	0.27	0.81
Non-outbreak	420	6877	34040490	7091	985	86.11	16	6054	35	2	0.89	0.31	0.86
Non-outbreak	480	7522	37471113	7091	727	89.75	18	6306	37	4	0.82	0.33	0.89
Non-outbreak	540	8306	41387560	7091	552	92.22	18	6483	34	5	0.78	0.35	0.92
Non-outbreak	600	9032	45052523	7091	395	94.43	20	6643	28	6	0.77	0.42	0.94
Non-outbreak	660	9682	48325820	7091	304	95.71	20	6735	27	6	0.77	0.43	0.95
Non-outbreak	720	10262	51312827	7091	262	96.31	20	6783	21	6	0.77	0.49	0.96
Non-outbreak	780	10845	54417219	7091	202	97.15	21	6845	18	6	0.78	0.54	0.97
Non-outbreak	840	11346	57135819	7091	178	97.49	22	6870	16	6	0.79	0.58	0.97
Non-outbreak	900	11793	59514439	7091	145	97.96	23	6898	18	8	0.74	0.56	0.98
Non-outbreak	960	12192	61590631	7091	111	98.43	22	6932	19	8	0.73	0.54	0.98
Non-outbreak	1020	12571	63597395	7091	99	98.60	22	6944	19	8	0.73	0.54	0.98
Non-outbreak	1080	12926	65415215	7091	87	98.77	21	6959	18	7	0.75	0.54	0.98
Non-outbreak	1140	13263	67138579	7091	71	99.00	22	6976	15	8	0.73	0.59	0.99
Non-outbreak	1200	13594	68911549	7091	62	99.13	22	6985	15	8	0.73	0.59	0.99
Non-outbreak	1260	13881	70408443	7091	59	99.17	22	6992	11	8	0.73	0.67	0.99
Non-outbreak	1320	14186	72080944	7091	53	99.25	23	7001	8	7	0.77	0.74	0.99
Non-outbreak	1380	14471	73573256	7091	44	99.38	23	7008	10	7	0.77	0.70	0.99
Non-outbreak	1440	14683	74801565	7091	40	99.44	23	7012	10	7	0.77	0.70	0.99

The columns show (from left to right): (1) the sample analysed; (2) the cumulative results at this time period (min); (3) the total number of two-direction reads; (4) the total number of nucleotide bases; (5) the total size of the alignment; (6) the number of bases in the alignment missing from the dataset; (7) the percentage of bases in the alignment that can be called; (8) the count of true positives; (9) the count of true negatives; (10) the count of false positives; (11) the count of false negatives; (12) the recall, that is, sensitivity, calculated as TP/(TP + FN); (13) the precision, calculated as TP/(TP + FP); (14) the accuracy, calculated as (TP + TN)/(P + N)

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