BamQC report
-----------------------------------

>>>>>>> Input

     bam file = output/mappings/longReadMapping/pacBio-Cshl-CapTrap_HpreCap_0+_Brain01Rep1.bam
     outfile = output/mappings/longReadMapping/bamqc/pacBio-Cshl-CapTrap_HpreCap_0+_Brain01Rep1/genome_results.txt


>>>>>>> Reference

     number of bases = 3,110,632,377 bp
     number of contigs = 288


>>>>>>> Globals

     number of windows = 687

     number of reads = 570,207
     number of mapped reads = 570,207 (100%)
     number of secondary alignments = 0

     number of mapped bases = 7,603,988,465 bp
     number of sequenced bases = 528,176,733 bp
     number of aligned bases = 0 bp
     number of duplicated reads (estimated) = 479,331
     duplication rate = 35.18%


>>>>>>> Insert size

     mean insert size = 0
     std insert size = 0
     median insert size = 0


>>>>>>> Mapping quality

     mean mapping quality = 2.4719


>>>>>>> ACTG content

     number of A's = 131,584,742 bp (24.91%)
     number of C's = 132,045,460 bp (25%)
     number of T's = 132,804,159 bp (25.14%)
     number of G's = 131,742,372 bp (24.94%)
     number of N's = 0 bp (0%)

     GC percentage = 49.94%


>>>>>>> Mismatches and indels

    general error rate = 0.0003
    number of mismatches = 1,193,137
    number of insertions = 751,197
    mapped reads with insertion percentage = 22.73%
    number of deletions = 228,576
    mapped reads with deletion percentage = 17.37%
    homopolymer indels = 36.68%


>>>>>>> Coverage

     mean coverageData = 2.4445X
     std coverageData = 13.5412X

     There is a 0.82% of reference with a coverageData >= 1X
     There is a 0.43% of reference with a coverageData >= 2X
     There is a 0.32% of reference with a coverageData >= 3X
     There is a 0.26% of reference with a coverageData >= 4X
     There is a 0.22% of reference with a coverageData >= 5X
     There is a 0.2% of reference with a coverageData >= 6X
     There is a 0.18% of reference with a coverageData >= 7X
     There is a 0.17% of reference with a coverageData >= 8X
     There is a 0.15% of reference with a coverageData >= 9X
     There is a 0.14% of reference with a coverageData >= 10X
     There is a 0.14% of reference with a coverageData >= 11X
     There is a 0.13% of reference with a coverageData >= 12X
     There is a 0.12% of reference with a coverageData >= 13X
     There is a 0.11% of reference with a coverageData >= 14X
     There is a 0.11% of reference with a coverageData >= 15X
     There is a 0.1% of reference with a coverageData >= 16X
     There is a 0.1% of reference with a coverageData >= 17X
     There is a 0.1% of reference with a coverageData >= 18X
     There is a 0.09% of reference with a coverageData >= 19X
     There is a 0.09% of reference with a coverageData >= 20X
     There is a 0.09% of reference with a coverageData >= 21X
     There is a 0.08% of reference with a coverageData >= 22X
     There is a 0.08% of reference with a coverageData >= 23X
     There is a 0.08% of reference with a coverageData >= 24X
     There is a 0.08% of reference with a coverageData >= 25X
     There is a 0.08% of reference with a coverageData >= 26X
     There is a 0.07% of reference with a coverageData >= 27X
     There is a 0.07% of reference with a coverageData >= 28X
     There is a 0.07% of reference with a coverageData >= 29X
     There is a 0.07% of reference with a coverageData >= 30X
     There is a 0.07% of reference with a coverageData >= 31X
     There is a 0.07% of reference with a coverageData >= 32X
     There is a 0.06% of reference with a coverageData >= 33X
     There is a 0.06% of reference with a coverageData >= 34X
     There is a 0.06% of reference with a coverageData >= 35X
     There is a 0.06% of reference with a coverageData >= 36X
     There is a 0.06% of reference with a coverageData >= 37X
     There is a 0.06% of reference with a coverageData >= 38X
     There is a 0.06% of reference with a coverageData >= 39X
     There is a 0.06% of reference with a coverageData >= 40X
     There is a 0.06% of reference with a coverageData >= 41X
     There is a 0.05% of reference with a coverageData >= 42X
     There is a 0.05% of reference with a coverageData >= 43X
     There is a 0.05% of reference with a coverageData >= 44X
     There is a 0.05% of reference with a coverageData >= 45X
     There is a 0.05% of reference with a coverageData >= 46X
     There is a 0.05% of reference with a coverageData >= 47X
     There is a 0.05% of reference with a coverageData >= 48X
     There is a 0.05% of reference with a coverageData >= 49X
     There is a 0.05% of reference with a coverageData >= 50X
     There is a 0.05% of reference with a coverageData >= 51X


>>>>>>> Coverage per contig

	chr1	248956422	719062601	2.88830709898297	11.194067780944474
	chr10	133797422	227956131	1.703740831419009	5.832588968411748
	chr11	135086622	363516057	2.6909848778363856	14.304491386629932
	chr12	133275309	451786857	3.3898766424919713	25.58492768113495
	chr13	114364328	106508040	0.9313047334130272	6.967769474296787
	chr14	107043718	255099661	2.383135281231543	15.72619653786268
	chr15	101991189	232822380	2.282769543945605	14.0010450820046
	chr16	90338345	228704816	2.5316471759583377	15.455715722048238
	chr17	83257441	272648781	3.274767729169096	18.237408010626094
	chr18	80373285	283641913	3.529057111451896	26.38344671548276
	chr19	58617616	391085354	6.671805861227792	26.879719005701553
	chr2	242193529	691150836	2.8537130568835307	12.18447692745895
	chr20	64444167	306347941	4.753695412030075	10.54697660283614
	chr21	46709983	127016449	2.7192570162142853	15.69159388152887
	chr22	50818468	152479336	3.000470931158334	16.5345080421014
	chr3	198295559	553076933	2.789154410664336	8.904508056985303
	chr4	190214555	336732318	1.7702762966798202	10.818767725053746
	chr5	181538259	408731266	2.251488299224022	7.848432217008903
	chr6	170805979	301024503	1.7623768486464986	11.165688433793374
	chr7	159345973	363201186	2.2793245361776417	14.287050428156164
	chr8	145138636	354255241	2.440805913320007	9.307875492903516
	chr9	138394717	200775129	1.4507427259669168	11.821495539947774
	chrIS	10567884	0	0.0	0.0
	chrM	16569	690877	41.69696421027219	30.0633936175228
	chrX	156040895	263499853	1.688658944182549	11.0548939104113
	chrY	57227415	10525331	0.1839211329045703	1.0115885302772625
	ERCC-00002	1061	0	0.0	0.0
	ERCC-00003	1023	0	0.0	0.0
	ERCC-00004	523	0	0.0	0.0
	ERCC-00009	984	0	0.0	0.0
	ERCC-00012	994	0	0.0	0.0
	ERCC-00013	808	0	0.0	0.0
	ERCC-00014	1957	0	0.0	0.0
	ERCC-00016	844	0	0.0	0.0
	ERCC-00017	1136	0	0.0	0.0
	ERCC-00019	644	0	0.0	0.0
	ERCC-00022	751	0	0.0	0.0
	ERCC-00024	536	0	0.0	0.0
	ERCC-00025	1994	0	0.0	0.0
	ERCC-00028	1130	0	0.0	0.0
	ERCC-00031	1138	0	0.0	0.0
	ERCC-00033	2022	0	0.0	0.0
	ERCC-00034	1019	0	0.0	0.0
	ERCC-00035	1130	0	0.0	0.0
	ERCC-00039	740	0	0.0	0.0
	ERCC-00040	744	0	0.0	0.0
	ERCC-00041	1122	0	0.0	0.0
	ERCC-00042	1023	0	0.0	0.0
	ERCC-00043	1023	0	0.0	0.0
	ERCC-00044	1156	0	0.0	0.0
	ERCC-00046	522	0	0.0	0.0
	ERCC-00048	992	0	0.0	0.0
	ERCC-00051	274	0	0.0	0.0
	ERCC-00053	1023	0	0.0	0.0
	ERCC-00054	274	0	0.0	0.0
	ERCC-00057	1021	0	0.0	0.0
	ERCC-00058	1136	0	0.0	0.0
	ERCC-00059	525	0	0.0	0.0
	ERCC-00060	523	0	0.0	0.0
	ERCC-00061	1136	0	0.0	0.0
	ERCC-00062	1023	0	0.0	0.0
	ERCC-00067	644	0	0.0	0.0
	ERCC-00069	1137	0	0.0	0.0
	ERCC-00071	642	0	0.0	0.0
	ERCC-00073	603	0	0.0	0.0
	ERCC-00074	522	0	0.0	0.0
	ERCC-00075	1023	0	0.0	0.0
	ERCC-00076	642	0	0.0	0.0
	ERCC-00077	273	0	0.0	0.0
	ERCC-00078	993	0	0.0	0.0
	ERCC-00079	644	0	0.0	0.0
	ERCC-00081	534	0	0.0	0.0
	ERCC-00083	1022	0	0.0	0.0
	ERCC-00084	994	0	0.0	0.0
	ERCC-00085	844	0	0.0	0.0
	ERCC-00086	1020	0	0.0	0.0
	ERCC-00092	1124	0	0.0	0.0
	ERCC-00095	521	0	0.0	0.0
	ERCC-00096	1107	0	0.0	0.0
	ERCC-00097	523	0	0.0	0.0
	ERCC-00098	1143	0	0.0	0.0
	ERCC-00099	1350	0	0.0	0.0
	ERCC-00104	2022	0	0.0	0.0
	ERCC-00108	1022	0	0.0	0.0
	ERCC-00109	536	0	0.0	0.0
	ERCC-00111	994	0	0.0	0.0
	ERCC-00112	1136	0	0.0	0.0
	ERCC-00113	840	0	0.0	0.0
	ERCC-00116	1991	0	0.0	0.0
	ERCC-00117	1136	0	0.0	0.0
	ERCC-00120	536	0	0.0	0.0
	ERCC-00123	1022	0	0.0	0.0
	ERCC-00126	1118	0	0.0	0.0
	ERCC-00130	1059	0	0.0	0.0
	ERCC-00131	771	0	0.0	0.0
	ERCC-00134	274	0	0.0	0.0
	ERCC-00136	1033	0	0.0	0.0
	ERCC-00137	537	0	0.0	0.0
	ERCC-00138	1024	0	0.0	0.0
	ERCC-00142	493	0	0.0	0.0
	ERCC-00143	784	0	0.0	0.0
	ERCC-00144	538	0	0.0	0.0
	ERCC-00145	1042	0	0.0	0.0
	ERCC-00147	1023	0	0.0	0.0
	ERCC-00148	494	0	0.0	0.0
	ERCC-00150	743	0	0.0	0.0
	ERCC-00154	537	0	0.0	0.0
	ERCC-00156	494	0	0.0	0.0
	ERCC-00157	1019	0	0.0	0.0
	ERCC-00158	1027	0	0.0	0.0
	ERCC-00160	743	0	0.0	0.0
	ERCC-00162	523	0	0.0	0.0
	ERCC-00163	543	0	0.0	0.0
	ERCC-00164	1022	0	0.0	0.0
	ERCC-00165	872	0	0.0	0.0
	ERCC-00168	1024	0	0.0	0.0
	ERCC-00170	1023	0	0.0	0.0
	ERCC-00171	505	0	0.0	0.0
	GL000008.2	209709	0	0.0	0.0
	GL000009.2	201709	0	0.0	0.0
	GL000194.1	191469	245884	1.2841974418835425	1.2890927705871833
	GL000195.1	182896	99483	0.5439320706849794	0.6006748740672874
	GL000205.2	185591	9106	0.04906487922366925	0.18281278269898876
	GL000208.1	92689	0	0.0	0.0
	GL000213.1	164239	0	0.0	0.0
	GL000214.1	137718	0	0.0	0.0
	GL000216.2	176608	0	0.0	0.0
	GL000218.1	161147	0	0.0	0.0
	GL000219.1	179198	338209	1.8873480730811727	2.0668000850148887
	GL000220.1	161802	9397	0.05807715603020976	0.19794258071308998
	GL000221.1	155397	57737	0.37154513922405197	0.3742429596445884
	GL000224.1	179693	7542	0.04197158486975008	0.09308152165799914
	GL000225.1	211173	0	0.0	0.0
	GL000226.1	15008	0	0.0	0.0
	KI270302.1	2274	0	0.0	0.0
	KI270303.1	1942	0	0.0	0.0
	KI270304.1	2165	0	0.0	0.0
	KI270305.1	1472	0	0.0	0.0
	KI270310.1	1201	0	0.0	0.0
	KI270311.1	12399	0	0.0	0.0
	KI270312.1	998	0	0.0	0.0
	KI270315.1	2276	0	0.0	0.0
	KI270316.1	1444	0	0.0	0.0
	KI270317.1	37690	0	0.0	0.0
	KI270320.1	4416	0	0.0	0.0
	KI270322.1	21476	0	0.0	0.0
	KI270329.1	1040	0	0.0	0.0
	KI270330.1	1652	0	0.0	0.0
	KI270333.1	2699	0	0.0	0.0
	KI270334.1	1368	0	0.0	0.0
	KI270335.1	1048	0	0.0	0.0
	KI270336.1	1026	0	0.0	0.0
	KI270337.1	1121	0	0.0	0.0
	KI270338.1	1428	0	0.0	0.0
	KI270340.1	1428	0	0.0	0.0
	KI270362.1	3530	0	0.0	0.0
	KI270363.1	1803	0	0.0	0.0
	KI270364.1	2855	0	0.0	0.0
	KI270366.1	8320	0	0.0	0.0
	KI270371.1	2805	0	0.0	0.0
	KI270372.1	1650	0	0.0	0.0
	KI270373.1	1451	0	0.0	0.0
	KI270374.1	2656	0	0.0	0.0
	KI270375.1	2378	0	0.0	0.0
	KI270376.1	1136	0	0.0	0.0
	KI270378.1	1048	0	0.0	0.0
	KI270379.1	1045	0	0.0	0.0
	KI270381.1	1930	0	0.0	0.0
	KI270382.1	4215	0	0.0	0.0
	KI270383.1	1750	0	0.0	0.0
	KI270384.1	1658	0	0.0	0.0
	KI270385.1	990	0	0.0	0.0
	KI270386.1	1788	0	0.0	0.0
	KI270387.1	1537	0	0.0	0.0
	KI270388.1	1216	0	0.0	0.0
	KI270389.1	1298	0	0.0	0.0
	KI270390.1	2387	0	0.0	0.0
	KI270391.1	1484	0	0.0	0.0
	KI270392.1	971	0	0.0	0.0
	KI270393.1	1308	0	0.0	0.0
	KI270394.1	970	0	0.0	0.0
	KI270395.1	1143	0	0.0	0.0
	KI270396.1	1880	0	0.0	0.0
	KI270411.1	2646	0	0.0	0.0
	KI270412.1	1179	0	0.0	0.0
	KI270414.1	2489	0	0.0	0.0
	KI270417.1	2043	0	0.0	0.0
	KI270418.1	2145	0	0.0	0.0
	KI270419.1	1029	0	0.0	0.0
	KI270420.1	2321	0	0.0	0.0
	KI270422.1	1445	0	0.0	0.0
	KI270423.1	981	0	0.0	0.0
	KI270424.1	2140	0	0.0	0.0
	KI270425.1	1884	0	0.0	0.0
	KI270429.1	1361	0	0.0	0.0
	KI270435.1	92983	0	0.0	0.0
	KI270438.1	112505	0	0.0	0.0
	KI270442.1	392061	0	0.0	0.0
	KI270448.1	7992	0	0.0	0.0
	KI270465.1	1774	0	0.0	0.0
	KI270466.1	1233	0	0.0	0.0
	KI270467.1	3920	0	0.0	0.0
	KI270468.1	4055	0	0.0	0.0
	KI270507.1	5353	0	0.0	0.0
	KI270508.1	1951	0	0.0	0.0
	KI270509.1	2318	0	0.0	0.0
	KI270510.1	2415	0	0.0	0.0
	KI270511.1	8127	0	0.0	0.0
	KI270512.1	22689	0	0.0	0.0
	KI270515.1	6361	0	0.0	0.0
	KI270516.1	1300	0	0.0	0.0
	KI270517.1	3253	0	0.0	0.0
	KI270518.1	2186	0	0.0	0.0
	KI270519.1	138126	0	0.0	0.0
	KI270521.1	7642	0	0.0	0.0
	KI270522.1	5674	0	0.0	0.0
	KI270528.1	2983	0	0.0	0.0
	KI270529.1	1899	0	0.0	0.0
	KI270530.1	2168	0	0.0	0.0
	KI270538.1	91309	0	0.0	0.0
	KI270539.1	993	0	0.0	0.0
	KI270544.1	1202	0	0.0	0.0
	KI270548.1	1599	0	0.0	0.0
	KI270579.1	31033	0	0.0	0.0
	KI270580.1	1553	0	0.0	0.0
	KI270581.1	7046	0	0.0	0.0
	KI270582.1	6504	0	0.0	0.0
	KI270583.1	1400	0	0.0	0.0
	KI270584.1	4513	0	0.0	0.0
	KI270587.1	2969	0	0.0	0.0
	KI270588.1	6158	0	0.0	0.0
	KI270589.1	44474	0	0.0	0.0
	KI270590.1	4685	0	0.0	0.0
	KI270591.1	5796	0	0.0	0.0
	KI270593.1	3041	0	0.0	0.0
	KI270706.1	175055	0	0.0	0.0
	KI270707.1	32032	0	0.0	0.0
	KI270708.1	127682	0	0.0	0.0
	KI270709.1	66860	0	0.0	0.0
	KI270710.1	40176	0	0.0	0.0
	KI270711.1	42210	0	0.0	0.0
	KI270712.1	176043	0	0.0	0.0
	KI270713.1	40745	1228	0.0301386673211437	0.17090132984990566
	KI270714.1	41717	0	0.0	0.0
	KI270715.1	161471	0	0.0	0.0
	KI270716.1	153799	0	0.0	0.0
	KI270717.1	40062	0	0.0	0.0
	KI270718.1	38054	0	0.0	0.0
	KI270719.1	176845	0	0.0	0.0
	KI270720.1	39050	0	0.0	0.0
	KI270721.1	100316	6154	0.06134614617807727	0.11576193745509722
	KI270722.1	194050	0	0.0	0.0
	KI270723.1	38115	0	0.0	0.0
	KI270724.1	39555	0	0.0	0.0
	KI270725.1	172810	0	0.0	0.0
	KI270726.1	43739	0	0.0	0.0
	KI270727.1	448248	0	0.0	0.0
	KI270728.1	1872759	0	0.0	0.0
	KI270729.1	280839	0	0.0	0.0
	KI270730.1	112551	0	0.0	0.0
	KI270731.1	150754	0	0.0	0.0
	KI270732.1	41543	0	0.0	0.0
	KI270733.1	179772	6174	0.034343501768907284	0.3414491277599925
	KI270734.1	165050	523441	3.1714086640412	7.522691870857001
	KI270735.1	42811	0	0.0	0.0
	KI270736.1	181920	0	0.0	0.0
	KI270737.1	103838	0	0.0	0.0
	KI270738.1	99375	0	0.0	0.0
	KI270739.1	73985	0	0.0	0.0
	KI270740.1	37240	0	0.0	0.0
	KI270741.1	157432	0	0.0	0.0
	KI270742.1	186739	0	0.0	0.0
	KI270743.1	210658	342978	1.6281271064948875	1.6229456310451333
	KI270744.1	168472	1342	0.007965715371100242	0.08889467222351889
	KI270745.1	41891	0	0.0	0.0
	KI270746.1	66486	0	0.0	0.0
	KI270747.1	198735	0	0.0	0.0
	KI270748.1	93321	0	0.0	0.0
	KI270749.1	158759	0	0.0	0.0
	KI270750.1	148850	0	0.0	0.0
	KI270751.1	150742	0	0.0	0.0
	KI270752.1	27745	0	0.0	0.0
	KI270753.1	62944	0	0.0	0.0
	KI270754.1	40191	0	0.0	0.0
	KI270755.1	36723	0	0.0	0.0
	KI270756.1	79590	0	0.0	0.0
	KI270757.1	71251	0	0.0	0.0
	SIRVome_isoforms	231019	0	0.0	0.0