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

>>>>>>> Input

     bam file = output/mappings/longReadMapping/ont-Crg-CapTrap_HpreCap_0+_Heart01Rep1.bam
     outfile = output/mappings/longReadMapping/bamqc/ont-Crg-CapTrap_HpreCap_0+_Heart01Rep1/genome_results.txt


>>>>>>> Reference

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


>>>>>>> Globals

     number of windows = 687

     number of reads = 341,313
     number of mapped reads = 341,313 (100%)
     number of secondary alignments = 0

     number of mapped bases = 2,905,871,039 bp
     number of sequenced bases = 220,370,342 bp
     number of aligned bases = 0 bp
     number of duplicated reads (estimated) = 289,096
     duplication rate = 32.77%


>>>>>>> Insert size

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


>>>>>>> Mapping quality

     mean mapping quality = 2.6222


>>>>>>> ACTG content

     number of A's = 53,360,244 bp (24.21%)
     number of C's = 55,143,725 bp (25.02%)
     number of T's = 56,756,641 bp (25.76%)
     number of G's = 55,109,732 bp (25.01%)
     number of N's = 0 bp (0%)

     GC percentage = 50.03%


>>>>>>> Mismatches and indels

    general error rate = 0.0045
    number of mismatches = 10,148,025
    number of insertions = 1,783,748
    mapped reads with insertion percentage = 95.21%
    number of deletions = 3,494,682
    mapped reads with deletion percentage = 99.19%
    homopolymer indels = 34.94%


>>>>>>> Coverage

     mean coverageData = 0.9342X
     std coverageData = 18.0053X

     There is a 0.34% of reference with a coverageData >= 1X
     There is a 0.17% of reference with a coverageData >= 2X
     There is a 0.12% of reference with a coverageData >= 3X
     There is a 0.1% of reference with a coverageData >= 4X
     There is a 0.08% of reference with a coverageData >= 5X
     There is a 0.07% of reference with a coverageData >= 6X
     There is a 0.06% of reference with a coverageData >= 7X
     There is a 0.06% of reference with a coverageData >= 8X
     There is a 0.05% of reference with a coverageData >= 9X
     There is a 0.05% of reference with a coverageData >= 10X
     There is a 0.05% of reference with a coverageData >= 11X
     There is a 0.04% of reference with a coverageData >= 12X
     There is a 0.04% of reference with a coverageData >= 13X
     There is a 0.04% of reference with a coverageData >= 14X
     There is a 0.04% of reference with a coverageData >= 15X
     There is a 0.03% of reference with a coverageData >= 16X
     There is a 0.03% of reference with a coverageData >= 17X
     There is a 0.03% of reference with a coverageData >= 18X
     There is a 0.03% of reference with a coverageData >= 19X
     There is a 0.03% of reference with a coverageData >= 20X
     There is a 0.03% of reference with a coverageData >= 21X
     There is a 0.03% of reference with a coverageData >= 22X
     There is a 0.03% of reference with a coverageData >= 23X
     There is a 0.03% of reference with a coverageData >= 24X
     There is a 0.02% of reference with a coverageData >= 25X
     There is a 0.02% of reference with a coverageData >= 26X
     There is a 0.02% of reference with a coverageData >= 27X
     There is a 0.02% of reference with a coverageData >= 28X
     There is a 0.02% of reference with a coverageData >= 29X
     There is a 0.02% of reference with a coverageData >= 30X
     There is a 0.02% of reference with a coverageData >= 31X
     There is a 0.02% of reference with a coverageData >= 32X
     There is a 0.02% of reference with a coverageData >= 33X
     There is a 0.02% of reference with a coverageData >= 34X
     There is a 0.02% of reference with a coverageData >= 35X
     There is a 0.02% of reference with a coverageData >= 36X
     There is a 0.02% of reference with a coverageData >= 37X
     There is a 0.02% of reference with a coverageData >= 38X
     There is a 0.02% of reference with a coverageData >= 39X
     There is a 0.02% of reference with a coverageData >= 40X
     There is a 0.02% of reference with a coverageData >= 41X
     There is a 0.02% of reference with a coverageData >= 42X
     There is a 0.02% of reference with a coverageData >= 43X
     There is a 0.02% of reference with a coverageData >= 44X
     There is a 0.02% of reference with a coverageData >= 45X
     There is a 0.02% of reference with a coverageData >= 46X
     There is a 0.01% of reference with a coverageData >= 47X
     There is a 0.01% of reference with a coverageData >= 48X
     There is a 0.01% of reference with a coverageData >= 49X
     There is a 0.01% of reference with a coverageData >= 50X
     There is a 0.01% of reference with a coverageData >= 51X


>>>>>>> Coverage per contig

	chr1	248956422	274765819	1.1036703403457493	6.950990596883335
	chr10	133797422	89311988	0.6675165086514149	3.424874384248648
	chr11	135086622	158696519	1.1747759818881252	14.761909797700824
	chr12	133275309	419416022	3.1469896798363455	76.85455363680438
	chr13	114364328	40315652	0.3525194674339362	6.502634169924749
	chr14	107043718	86167328	0.804973235328018	5.990686504544323
	chr15	101991189	93449059	0.9162463926173073	9.630264454137857
	chr16	90338345	55767494	0.6173180834782838	6.391544920576141
	chr17	83257441	80730246	0.9696460163842893	17.175230935236783
	chr18	80373285	36623439	0.45566681764967054	8.702279465732879
	chr19	58617616	161975673	2.763259307577435	14.826045660158423
	chr2	242193529	185412541	0.7655553051543338	11.01134716579426
	chr20	64444167	38056509	0.5905345785600735	5.030932026696382
	chr21	46709983	53537062	1.1461588842796195	7.663467761826787
	chr22	50818468	76990750	1.515015171256245	16.186461487159693
	chr3	198295559	159504718	0.8043786699227087	11.77836231747978
	chr4	190214555	138523128	0.7282467316972668	3.871046901610704
	chr5	181538259	165089052	0.9093898603489416	7.398810211731591
	chr6	170805979	143637026	0.8409367566693904	5.330875298193321
	chr7	159345973	136606040	0.8572920760288055	6.989260119037919
	chr8	145138636	145144170	1.0000381290616511	6.316926174153633
	chr9	138394717	67199775	0.4855660422355573	4.520579635421623
	chrIS	10567884	0	0.0	0.0
	chrM	16569	548497	33.10380831673607	38.59867346687529
	chrX	156040895	86632338	0.5551899583759757	5.667036605717527
	chrY	57227415	9899815	0.17299077723500178	1.0718215554041095
	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	645490	3.371250698546501	3.3693284042968203
	GL000195.1	182896	44942	0.24572434607645877	0.31870136451225045
	GL000205.2	185591	62270	0.3355227354774747	0.4412185983301368
	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	232735	1.4442403519767666	1.4577456485158926
	GL000219.1	179198	0	0.0	0.0
	GL000220.1	161802	35114	0.2170183310465878	0.8057304440125289
	GL000221.1	155397	0	0.0	0.0
	GL000224.1	179693	24163	0.13446823192890095	0.15742506239672985
	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	0	0.0	0.0
	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	173	0.0017245504206706806	0.04125176495805553
	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	23898	0.012760851770035546	0.051130583374430404
	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	41841	0.2327448100927842	0.7884096319426271
	KI270734.1	165050	19806	0.12	0.5376196033701717
	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	739947	3.9624663300114062	3.957846295288264
	KI270743.1	210658	0	0.0	0.0
	KI270744.1	168472	0	0.0	0.0
	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