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

>>>>>>> Input

     bam file = output/mappings/longReadMapping/ont-Crg-dRNA_HpreCap_0+_Brain03Rep1.bam
     outfile = output/mappings/longReadMapping/bamqc/ont-Crg-dRNA_HpreCap_0+_Brain03Rep1/genome_results.txt


>>>>>>> Reference

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


>>>>>>> Globals

     number of windows = 687

     number of reads = 62,019
     number of mapped reads = 62,019 (100%)
     number of secondary alignments = 0

     number of mapped bases = 180,052,037 bp
     number of sequenced bases = 37,493,423 bp
     number of aligned bases = 0 bp
     number of duplicated reads (estimated) = 29,869
     duplication rate = 20.97%


>>>>>>> Insert size

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


>>>>>>> Mapping quality

     mean mapping quality = 6.9673


>>>>>>> ACTG content

     number of A's = 9,876,373 bp (26.34%)
     number of C's = 10,540,352 bp (28.11%)
     number of T's = 8,884,594 bp (23.7%)
     number of G's = 8,192,104 bp (21.85%)
     number of N's = 0 bp (0%)

     GC percentage = 49.96%


>>>>>>> Mismatches and indels

    general error rate = 0.0231
    number of mismatches = 3,200,457
    number of insertions = 645,543
    mapped reads with insertion percentage = 98.86%
    number of deletions = 1,259,380
    mapped reads with deletion percentage = 99.95%
    homopolymer indels = 36.88%


>>>>>>> Coverage

     mean coverageData = 0.0579X
     std coverageData = 2.5092X

     There is a 0.24% of reference with a coverageData >= 1X
     There is a 0.1% of reference with a coverageData >= 2X
     There is a 0.06% of reference with a coverageData >= 3X
     There is a 0.04% of reference with a coverageData >= 4X
     There is a 0.03% of reference with a coverageData >= 5X
     There is a 0.02% of reference with a coverageData >= 6X
     There is a 0.02% of reference with a coverageData >= 7X
     There is a 0.02% of reference with a coverageData >= 8X
     There is a 0.01% of reference with a coverageData >= 9X
     There is a 0.01% of reference with a coverageData >= 10X
     There is a 0.01% of reference with a coverageData >= 11X
     There is a 0.01% of reference with a coverageData >= 12X
     There is a 0.01% of reference with a coverageData >= 13X
     There is a 0.01% of reference with a coverageData >= 14X
     There is a 0.01% of reference with a coverageData >= 15X
     There is a 0.01% of reference with a coverageData >= 16X
     There is a 0.01% of reference with a coverageData >= 17X
     There is a 0.01% of reference with a coverageData >= 18X
     There is a 0.01% of reference with a coverageData >= 19X
     There is a 0.01% of reference with a coverageData >= 20X
     There is a 0.01% of reference with a coverageData >= 21X
     There is a 0.01% of reference with a coverageData >= 22X
     There is a 0% of reference with a coverageData >= 23X
     There is a 0% of reference with a coverageData >= 24X
     There is a 0% of reference with a coverageData >= 25X
     There is a 0% of reference with a coverageData >= 26X
     There is a 0% of reference with a coverageData >= 27X
     There is a 0% of reference with a coverageData >= 28X
     There is a 0% of reference with a coverageData >= 29X
     There is a 0% of reference with a coverageData >= 30X
     There is a 0% of reference with a coverageData >= 31X
     There is a 0% of reference with a coverageData >= 32X
     There is a 0% of reference with a coverageData >= 33X
     There is a 0% of reference with a coverageData >= 34X
     There is a 0% of reference with a coverageData >= 35X
     There is a 0% of reference with a coverageData >= 36X
     There is a 0% of reference with a coverageData >= 37X
     There is a 0% of reference with a coverageData >= 38X
     There is a 0% of reference with a coverageData >= 39X
     There is a 0% of reference with a coverageData >= 40X
     There is a 0% of reference with a coverageData >= 41X
     There is a 0% of reference with a coverageData >= 42X
     There is a 0% of reference with a coverageData >= 43X
     There is a 0% of reference with a coverageData >= 44X
     There is a 0% of reference with a coverageData >= 45X
     There is a 0% of reference with a coverageData >= 46X
     There is a 0% of reference with a coverageData >= 47X
     There is a 0% of reference with a coverageData >= 48X
     There is a 0% of reference with a coverageData >= 49X
     There is a 0% of reference with a coverageData >= 50X
     There is a 0% of reference with a coverageData >= 51X


>>>>>>> Coverage per contig

	chr1	248956422	14372514	0.05773104338718364	0.29079625060219133
	chr10	133797422	5921004	0.044253498397001996	0.27545409829667095
	chr11	135086622	11668209	0.08637575525428418	0.9068387513906296
	chr12	133275309	7251232	0.054407917373502396	0.6432184292251049
	chr13	114364328	2184627	0.019102346319037525	0.08297316780062398
	chr14	107043718	4524414	0.04226697357429233	0.4176244937601639
	chr15	101991189	3842127	0.03767116588865338	0.3006236162471301
	chr16	90338345	8185774	0.09061239720519565	0.6584117067081074
	chr17	83257441	8614701	0.10347064354283961	0.8487814744255412
	chr18	80373285	9229089	0.11482781872110864	3.572689831826905
	chr19	58617616	14611891	0.24927474020779009	1.060831302474714
	chr2	242193529	11043288	0.045596957299383505	0.3163517988487718
	chr20	64444167	5761940	0.08940979871770241	0.6947808268188448
	chr21	46709983	2131270	0.045627719453462445	0.24653367884619562
	chr22	50818468	4758382	0.09363489666788066	0.40057356712376035
	chr3	198295559	9610434	0.04846520037294431	0.29324192368757335
	chr4	190214555	3909006	0.020550509397138404	0.18414150076158983
	chr5	181538259	7985319	0.04398697577021492	0.22929321340248912
	chr6	170805979	6299447	0.036880717155691606	0.2773744113535125
	chr7	159345973	6919981	0.043427398067976276	0.328122782939754
	chr8	145138636	6777265	0.04669511294015468	0.5053748790901039
	chr9	138394717	6962028	0.050305590783497896	0.43112047696099554
	chrIS	10567884	0	0.0	0.0
	chrM	16569	13707650	827.3070191321142	704.2050473429663
	chrX	156040895	3575095	0.022911269510470317	0.2673781656183501
	chrY	57227415	121800	0.002128350546674177	0.023550632357465556
	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	351	0.0018331949297275276	0.04191638727673976
	GL000195.1	182896	0	0.0	0.0
	GL000205.2	185591	0	0.0	0.0
	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	384	0.00214288105894039	0.04496223476597227
	GL000220.1	161802	30882	0.19086290651537063	0.26308451289353485
	GL000221.1	155397	0	0.0	0.0
	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	558	0.013219616204690832	0.11145452522189785
	KI270712.1	176043	247	0.0014030662963026078	0.036666780581122604
	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	9176	0.09147095179233622	0.11767928677302576
	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	4488	0.02496495561043989	0.31273556720966794
	KI270734.1	165050	37464	0.22698576189033626	0.3746171058537016
	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	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