Qualimap report: Multi-sample BAM QC

Input data and parameters

Samples (with groups)

Sample8 (16C_32psu)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_32psu_4_S4.sorted_stats
Sample9 (8C_26psu)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/8C_26psu_1_S9.sorted_stats
Sample13 (8C_32psu)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/8C_32psu_1_S5.sorted_stats
Sample17 (CTRL_16)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19.sorted_stats
Sample20 (CTRL_8)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18.sorted_stats
Sample7 (16C_32psu)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_32psu_3_S3.sorted_stats
Sample18 (CTRL_16)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21.sorted_stats
Sample4 (16C_26psu)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_26psu_4_S16.sorted_stats
Sample11 (8C_26psu)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/8C_26psu_3_S11.sorted_stats
Sample3 (16C_26psu)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_26psu_3_S15.sorted_stats
Sample6 (16C_32psu)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_32psu_2_S2.sorted_stats
Sample15 (8C_32psu)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/8C_32psu_3_S7.sorted_stats
Sample19 (CTRL_8)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17.sorted_stats
Sample5 (16C_32psu)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_32psu_1_S1.sorted_stats
Sample1 (16C_26psu)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_26psu_1_S13.sorted_stats
Sample2 (16C_26psu)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/16C_26psu_2_S14.sorted_stats
Sample14 (8C_32psu)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/8C_32psu_2_S6.sorted_stats
Sample16 (8C_32psu)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/8C_32psu_4_S8.sorted_stats
Sample10 (8C_26psu)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/8C_26psu_2_S10.sorted_stats
Sample12 (8C_26psu)	/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190828_Salmo/8C_26psu_4_S12.sorted_stats

Summary

Globals

Number of samples	20
Number of groups	6
Total number of mapped reads	650,900,822
Mean samples coverage	1.53
Mean samples GC-content	27.35
Mean samples mapping quality	23.64
Mean samples insert size	113

Sample statistics

Sample	Group	Coverage mean	Coverage std	GC percentage	Mapping quality mean	Insert size median
Sample1	16C_26psu	2.0853	15.4161	27.04	23.5337	116.0
Sample2	16C_26psu	1.6893	11.4299	27.09	23.6838	120.0
Sample3	16C_26psu	1.4876	11.1563	27.83	23.665	126.0
Sample4	16C_26psu	1.6261	10.5899	27.39	24.1154	113.0
Sample5	16C_32psu	1.7658	12.6447	27.58	23.5487	104.0
Sample6	16C_32psu	1.7683	13.8162	27.56	23.9112	108.0
Sample7	16C_32psu	1.2682	10.7154	27.99	23.5231	103.0
Sample8	16C_32psu	1.6248	8.5179	25.75	24.5146	133.0
Sample9	8C_26psu	1.7581	12.0456	27.13	23.5599	120.0
Sample10	8C_26psu	1.8514	12.4513	27.02	24.2685	113.0
Sample11	8C_26psu	1.5631	13.4152	28.39	23.1084	101.0
Sample12	8C_26psu	1.34	13.3278	25.44	23.7412	139.0
Sample13	8C_32psu	1.1681	10.6826	28.97	23.447	93.0
Sample14	8C_32psu	1.2305	8.3116	27.26	24.1981	113.0
Sample15	8C_32psu	1.3028	10.0034	27.68	23.7431	106.0
Sample16	8C_32psu	1.4312	11.4631	26.13	23.0811	122.0
Sample17	CTRL_16	1.6756	12.7065	27.31	23.1111	115.0
Sample18	CTRL_16	1.1158	10.7513	29.03	21.0849	100.0
Sample19	CTRL_8	1.4311	11.9724	25.2	25.3122	123.0
Sample20	CTRL_8	1.4032	12.8932	29.24	23.5659	92.0