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

>>>>>>> Input

     bam file = output/mappings/longReadMapping/ont-Cshl-dRNA_HpreCap_0+_Heart01Rep1.bam
     outfile = output/mappings/longReadMapping/bamqc/ont-Cshl-dRNA_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 = 839,770
     number of mapped reads = 839,770 (100%)
     number of secondary alignments = 0

     number of mapped bases = 2,837,706,386 bp
     number of sequenced bases = 461,999,231 bp
     number of aligned bases = 0 bp
     number of duplicated reads (estimated) = 632,641
     duplication rate = 24.97%


>>>>>>> Insert size

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


>>>>>>> Mapping quality

     mean mapping quality = 5.0471


>>>>>>> ACTG content

     number of A's = 131,123,044 bp (28.38%)
     number of C's = 113,123,253 bp (24.49%)
     number of T's = 115,951,654 bp (25.1%)
     number of G's = 101,801,280 bp (22.03%)
     number of N's = 0 bp (0%)

     GC percentage = 46.52%


>>>>>>> Mismatches and indels

    general error rate = 0.0157
    number of mismatches = 32,995,473
    number of insertions = 7,671,917
    mapped reads with insertion percentage = 98.38%
    number of deletions = 13,315,324
    mapped reads with deletion percentage = 99.81%
    homopolymer indels = 38.05%


>>>>>>> Coverage

     mean coverageData = 0.9123X
     std coverageData = 49.785X

     There is a 0.84% of reference with a coverageData >= 1X
     There is a 0.49% of reference with a coverageData >= 2X
     There is a 0.37% of reference with a coverageData >= 3X
     There is a 0.3% of reference with a coverageData >= 4X
     There is a 0.25% of reference with a coverageData >= 5X
     There is a 0.22% of reference with a coverageData >= 6X
     There is a 0.19% 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 0.13% of reference with a coverageData >= 11X
     There is a 0.12% of reference with a coverageData >= 12X
     There is a 0.11% of reference with a coverageData >= 13X
     There is a 0.1% of reference with a coverageData >= 14X
     There is a 0.1% 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 0.08% 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 0.05% of reference with a coverageData >= 26X
     There is a 0.05% 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 0.04% of reference with a coverageData >= 32X
     There is a 0.04% of reference with a coverageData >= 33X
     There is a 0.04% of reference with a coverageData >= 34X
     There is a 0.04% of reference with a coverageData >= 35X
     There is a 0.04% 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 0.03% of reference with a coverageData >= 41X
     There is a 0.03% of reference with a coverageData >= 42X
     There is a 0.03% of reference with a coverageData >= 43X
     There is a 0.03% of reference with a coverageData >= 44X
     There is a 0.03% of reference with a coverageData >= 45X
     There is a 0.03% of reference with a coverageData >= 46X
     There is a 0.03% of reference with a coverageData >= 47X
     There is a 0.03% of reference with a coverageData >= 48X
     There is a 0.03% 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	253273309	1.017339930279043	13.300427301806556
	chr10	133797422	103101268	0.7705773882549097	3.766622978166651
	chr11	135086622	134133923	0.9929474955706569	10.040655379716245
	chr12	133275309	169246578	1.2699019741158506	16.496682105706515
	chr13	114364328	43065086	0.3765604778441054	3.788767094638196
	chr14	107043718	70336722	0.6570840710147979	7.634195603301303
	chr15	101991189	146990626	1.44120906365745	18.467269265315622
	chr16	90338345	66267849	0.7335517271209695	6.2017846239201155
	chr17	83257441	85772176	1.0302043273225272	7.80878196957714
	chr18	80373285	56489679	0.7028414852024525	13.353894788929486
	chr19	58617616	151042711	2.576746058727465	17.1925126878379
	chr2	242193529	215500961	0.8897882692811334	9.540193689681333
	chr20	64444167	49224685	0.7638346074051977	5.094807034917177
	chr21	46709983	26789714	0.5735329426259906	2.790397993305209
	chr22	50818468	83154478	1.6363043057496343	23.59052232522478
	chr3	198295559	139378055	0.7028803655658269	9.690327577904194
	chr4	190214555	133963198	0.7042741708172647	4.6337696064788885
	chr5	181538259	150242305	0.8276068407155981	4.274730274808965
	chr6	170805979	122644655	0.7180349055579606	4.836430478142964
	chr7	159345973	120003526	0.7531004627271001	4.764974740575584
	chr8	145138636	129078272	0.889344667673465	4.152602988806299
	chr9	138394717	76925545	0.5558416294171113	3.605638807536738
	chrIS	10567884	0	0.0	0.0
	chrM	16569	148281598	8949.33900657855	19600.150869238132
	chrX	156040895	73922954	0.4737408997814323	4.3603761859163574
	chrY	57227415	6098356	0.10656354126776475	0.6597398246944544
	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	334013	1.744475607017324	1.7409192133673748
	GL000195.1	182896	1693	0.009256626716822675	0.11572651652155223
	GL000205.2	185591	42686	0.23000037717346208	0.2485036028430041
	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	215695	1.3384983896690599	1.3194530613308049
	GL000219.1	179198	4548	0.025379747541825242	0.19337722957993947
	GL000220.1	161802	16400	0.10135845045178675	0.45541961051937935
	GL000221.1	155397	592	0.0038095973538742702	0.0592259218167498
	GL000224.1	179693	0	0.0	0.0
	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	323	0.007652215114901682	0.08372840894623457
	KI270712.1	176043	581	0.0033003300330033004	0.07416038476586023
	KI270713.1	40745	1056	0.02591729046508774	0.15413065414055227
	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	17126	0.17072052314685593	1.3779796009706906
	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	24486	0.013074827033270165	0.07417705599296487
	KI270729.1	280839	0	0.0	0.0
	KI270730.1	112551	0	0.0	0.0
	KI270731.1	150754	130	8.623320110909163E-4	0.02831945353317526
	KI270732.1	41543	0	0.0	0.0
	KI270733.1	179772	92804	0.516231671228	1.3862144116447377
	KI270734.1	165050	141946	0.860018176310209	1.870867620966762
	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	20610	0.11036794670636557	0.12820903245258097
	KI270743.1	210658	0	0.0	0.0
	KI270744.1	168472	1638	0.009722683888123843	0.11791181615294903
	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	272	0.0018044075307479003	0.04125533881940453
	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	81861558	354.34989329881955	369.73744853885626