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

>>>>>>> Input

     bam file = output/mappings/longReadMapping/pacBio-Cshl-CapTrap_HpreCap_0+_Heart01Rep1.bam
     outfile = output/mappings/longReadMapping/bamqc/pacBio-Cshl-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 = 463,064
     number of mapped reads = 463,064 (100%)
     number of secondary alignments = 0

     number of mapped bases = 6,390,169,619 bp
     number of sequenced bases = 451,257,756 bp
     number of aligned bases = 0 bp
     number of duplicated reads (estimated) = 402,936
     duplication rate = 35.96%


>>>>>>> Insert size

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


>>>>>>> Mapping quality

     mean mapping quality = 2.582


>>>>>>> ACTG content

     number of A's = 113,973,573 bp (25.26%)
     number of C's = 111,721,296 bp (24.76%)
     number of T's = 114,264,202 bp (25.32%)
     number of G's = 111,298,685 bp (24.66%)
     number of N's = 0 bp (0%)

     GC percentage = 49.42%


>>>>>>> Mismatches and indels

    general error rate = 0.0003
    number of mismatches = 942,189
    number of insertions = 589,457
    mapped reads with insertion percentage = 23.3%
    number of deletions = 183,456
    mapped reads with deletion percentage = 16.73%
    homopolymer indels = 37.51%


>>>>>>> Coverage

     mean coverageData = 2.0543X
     std coverageData = 31.1092X

     There is a 0.6% of reference with a coverageData >= 1X
     There is a 0.34% of reference with a coverageData >= 2X
     There is a 0.25% of reference with a coverageData >= 3X
     There is a 0.21% of reference with a coverageData >= 4X
     There is a 0.18% of reference with a coverageData >= 5X
     There is a 0.16% of reference with a coverageData >= 6X
     There is a 0.15% of reference with a coverageData >= 7X
     There is a 0.14% of reference with a coverageData >= 8X
     There is a 0.13% of reference with a coverageData >= 9X
     There is a 0.12% of reference with a coverageData >= 10X
     There is a 0.11% of reference with a coverageData >= 11X
     There is a 0.1% of reference with a coverageData >= 12X
     There is a 0.1% of reference with a coverageData >= 13X
     There is a 0.09% of reference with a coverageData >= 14X
     There is a 0.09% of reference with a coverageData >= 15X
     There is a 0.09% of reference with a coverageData >= 16X
     There is a 0.08% of reference with a coverageData >= 17X
     There is a 0.08% of reference with a coverageData >= 18X
     There is a 0.07% of reference with a coverageData >= 19X
     There is a 0.07% of reference with a coverageData >= 20X
     There is a 0.07% of reference with a coverageData >= 21X
     There is a 0.07% of reference with a coverageData >= 22X
     There is a 0.06% of reference with a coverageData >= 23X
     There is a 0.06% of reference with a coverageData >= 24X
     There is a 0.06% of reference with a coverageData >= 25X
     There is a 0.06% of reference with a coverageData >= 26X
     There is a 0.06% of reference with a coverageData >= 27X
     There is a 0.05% of reference with a coverageData >= 28X
     There is a 0.05% of reference with a coverageData >= 29X
     There is a 0.05% of reference with a coverageData >= 30X
     There is a 0.05% of reference with a coverageData >= 31X
     There is a 0.05% of reference with a coverageData >= 32X
     There is a 0.05% of reference with a coverageData >= 33X
     There is a 0.05% of reference with a coverageData >= 34X
     There is a 0.05% of reference with a coverageData >= 35X
     There is a 0.05% of reference with a coverageData >= 36X
     There is a 0.04% of reference with a coverageData >= 37X
     There is a 0.04% of reference with a coverageData >= 38X
     There is a 0.04% of reference with a coverageData >= 39X
     There is a 0.04% of reference with a coverageData >= 40X
     There is a 0.04% of reference with a coverageData >= 41X
     There is a 0.04% of reference with a coverageData >= 42X
     There is a 0.04% of reference with a coverageData >= 43X
     There is a 0.04% of reference with a coverageData >= 44X
     There is a 0.04% of reference with a coverageData >= 45X
     There is a 0.04% of reference with a coverageData >= 46X
     There is a 0.04% of reference with a coverageData >= 47X
     There is a 0.04% of reference with a coverageData >= 48X
     There is a 0.04% of reference with a coverageData >= 49X
     There is a 0.03% of reference with a coverageData >= 50X
     There is a 0.03% of reference with a coverageData >= 51X


>>>>>>> Coverage per contig

	chr1	248956422	656130892	2.6355250719340755	18.73959725697925
	chr10	133797422	228756865	1.7097255057724505	5.392918349269686
	chr11	135086622	356887715	2.6419175319966177	27.284543082072844
	chr12	133275309	832210193	6.244293854910515	132.35893067471966
	chr13	114364328	101575775	0.8881770808813741	14.905952201338868
	chr14	107043718	142665752	1.3327802384442589	3.838379580479903
	chr15	101991189	267069777	2.618557344203527	17.579098470090354
	chr16	90338345	128498871	1.4224178116169828	9.507544395972642
	chr17	83257441	158778662	1.9070807376844552	36.36155109860569
	chr18	80373285	102215420	1.2717586446790123	21.0509138752932
	chr19	58617616	227835429	3.886808173843167	20.475496006069413
	chr2	242193529	463895710	1.915392669306206	6.092083836145478
	chr20	64444167	96753159	1.501348585978309	4.5309475767834275
	chr21	46709983	71494757	1.530609784208228	8.706873631664493
	chr22	50818468	193182651	3.801426107532403	42.60925877504825
	chr3	198295559	365429846	1.8428544130935378	19.971343602709887
	chr4	190214555	408297058	2.146507968330815	5.748306255542891
	chr5	181538259	340218314	1.874086023927331	5.9859861296881665
	chr6	170805979	331192181	1.9389964153421118	8.99992978605395
	chr7	159345973	309020781	1.9393071263871853	8.856231632880093
	chr8	145138636	271650593	1.8716628493049914	5.397908617202973
	chr9	138394717	136074436	0.9832343238940255	7.104252506174467
	chrIS	10567884	0	0.0	0.0
	chrM	16569	593224	35.80324702758163	37.260451209513235
	chrX	156040895	181566323	1.1635816559498713	9.471649233680331
	chrY	57227415	16107362	0.2814623375876754	2.0958995798632007
	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	29972	0.14292185838471405	0.1640758237396107
	GL000009.2	201709	0	0.0	0.0
	GL000194.1	191469	832888	4.349988771028208	4.35566326515813
	GL000195.1	182896	78021	0.42658669407750854	0.4663780068541461
	GL000205.2	185591	50614	0.2727179658496371	0.6603966889363824
	GL000208.1	92689	0	0.0	0.0
	GL000213.1	164239	0	0.0	0.0
	GL000214.1	137718	37962	0.2756502417984577	0.2851034731771456
	GL000216.2	176608	0	0.0	0.0
	GL000218.1	161147	386670	2.399486183422589	2.3971561407502597
	GL000219.1	179198	112510	0.6278529894306856	0.6402739787237113
	GL000220.1	161802	6043	0.03734811683415533	0.2018857858400292
	GL000221.1	155397	0	0.0	0.0
	GL000224.1	179693	3053	0.016990088651199546	0.1709489333456923
	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	1286	0.030466714048803602	0.1718676624146382
	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	1042	0.01038717652218988	0.09331503635347167
	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	44116	0.023556688287174162	0.09001024002046315
	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	3641	0.020253432125136285	0.17913126651574038
	KI270734.1	165050	162981	0.9874644047258406	2.4308679025896898
	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	317074	1.6979527575921474	1.6937988469064442
	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