Table 1.

Benchmarking for the simulated dataset containing 10 million single-end reads simulated with the BEERS program

RL	MR (%)	HPG Aligner 1				HISAT				STAR 2				TopHat 2 + Bowtie 2				MapSplice 2
		IMR	RNM	CMR	T	IMR	RNM	CMR	T	IMR	RNM	CMR	T	IMR	RNM	CMR	T	IMR	RNM	CMR	T
	0.1	3.08	0.42	96.5	4.8	4.42	3.22	92.36	4.45	7.32	1.46	91.22	8.28	2.05	0.93	97.02	36.35	2.82	1.16	96.02	26.93
50	1	4.26	0.84	94.9	4.9	9.79	8.61	81.60	4.80	11.23	1.72	87.05	8.73	2.06	3.04	94.90	79.65	2.95	2.03	95.02	26.13
	2	5.82	2.26	91.92	5.2	16.29	17.18	66.53	4.58	15.44	3.16	81.40	8.85	2.00	10.18	87.82	374.9	3.21	4.81	91.98	26.08
	0.1	3.51	0.24	96.25	5.8	2.30	1.13	96.57	6.21	7.81	0.46	91.73	9.52	0.28	2.98	96.74	48.22	3.31	0.24	96.45	37.32
75	1	4.17	0.94	94.89	6.0	4.64	3.48	91.88	6.40	11.82	1.18	87.00	9.97	1.24	6.90	91.86	50.78	3.59	1.16	95.25	35.05
	2	5.64	1.27	93.09	6.4	10.59	10.46	78.95	6.46	16.62	1.55	81.83	11.25	0.94	22.18	76.88	58.93	5.13	2.20	92.67	34.28
	0.1	4.07	0.24	95.69	7.4	2.57	1.24	96.19	7.86	7.59	0.64	91.77	11.77	1.69	1.94	96.37	65.08	3.54	0.26	96.20	51.17
100	1	4.95	0.55	94.50	7.5	5.70	4.51	89.79	8.15	11.90	0.62	87.48	12.08	0.99	11.70	87.31	74.02	3.98	0.68	95.34	46.03
	2	6.07	0.93	93.00	7.8	15.64	17.19	67.17	8.40	16.48	1.14	82.38	12.35	0.60	36.14	63.26	85.65	6.45	1.50	92.05	45.6
	0.1	5.58	0.31	94.11	10.5	3.15	1.56	95.29	11.75	8.40	0.57	91.03	15.07	1.49	3.55	94.96	97.9	5.45	0.21	94.34	56.88
150	1	7.77	1.95	90.28	10.6	12.49	13.03	74.48	11.41	12.88	2.73	84.39	15.08	0.82	27.13	72.05	121.55	8.23	2.67	89.10	53.53
	2	7.06	0.78	92.16	10.9	24.42	39.76	35.82	11.91	15.97	0.73	83.30	15.73	0.45	61.84	37.71	140.28	13.65	1.57	84.78	56.73
	0.1	8.21	0.66	91.13	16.55	4.49	2.47	93.04	17.80	9.13	0.62	90.25	21.58	1.62	6.70	91.68	185.78	11.51	0.23	88.26	75.55
250	1	8.43	0.81	90.76	16.5	22.28	31.6	46.12	19.28	12.99	0.71	86.30	22.3	0.28	53.29	46.43	256.83	29.85	0.75	69.40	79.28
	2	8.72	1.62	89.66	17.45	17.75	77.04	5.21	17.46	18.35	1.43	80.22	23.35	0.07	89.62	10.31	309.85	35.27	1.24	63.49	76.37
	0.1	10.02	1.08	88.90	25.45	6.88	5.04	88.08	28.5	9.98	0.56	89.46	32.12	0.99	12.32	86.69	369.58	17.33	0.03	82.64	106.67
400	1	12.94	3.35	83.71	25.6	22.52	66.17	11.31	29.7	14.82	4.26	80.92	33.83	0.09	82.40	17.51	573.18	51.64	1.65	46.71	103.98
	2	11.78	2.84	85.38	26.0	3.08	96.82	0.10	27.10	32.75	2.75	64.5	24.5	0.01	99.02	0.97	603.28	54.34	0.51	45.15	106.53

First column, RL, indicated read length in bp. Second column represents the mutation rate (MR). For each program, the table contains the following columns with the percentages of: IMR: incorrectly mapped reads; RNM: reads not mapped; CMR: correctly mapped reads covering the corresponding splice junctions. The last column, T, represents runtimes for producing a BAM file in min.