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

>>>>>>> Input

     bam file = ../qualimap2/test-data/test.bam
     outfile = /Users/scott/qualimap_results/../qualimap2/test-data/test_stats/genome_results.txt


>>>>>>> Reference

     number of bases = 3,101,976,562 bp
     number of contigs = 85


>>>>>>> Globals

     number of windows = 484

     number of reads = 61,169
     number of mapped reads = 60,246 (98.49%)
     number of supplementary alignments = 1,169 (1.91%)
     number of secondary alignments = 0

     number of mapped paired reads (first in pair) = 30,268
     number of mapped paired reads (second in pair) = 29,978
     number of mapped paired reads (both in pair) = 59,810
     number of mapped paired reads (singletons) = 436

     number of mapped bases = 13,270,629 bp
     number of sequenced bases = 13,248,971 bp
     number of aligned bases = 0 bp
     number of duplicated reads (flagged) = 48


>>>>>>> Insert size

     mean insert size = 75,226.7884
     std insert size = 2,849,315.9638
     median insert size = 427


>>>>>>> Mapping quality

     mean mapping quality = 49.9688


>>>>>>> ACTG content

     number of A's = 3,912,917 bp (29.53%)
     number of C's = 2,699,395 bp (20.37%)
     number of T's = 3,942,019 bp (29.75%)
     number of G's = 2,694,640 bp (20.34%)
     number of N's = 14,397 bp (0.11%)

     GC percentage = 40.71%


>>>>>>> Mismatches and indels

    general error rate = 0.0149
    number of mismatches = 190,508
    number of insertions = 2,279
    mapped reads with insertion percentage = 3.3%
    number of deletions = 2,316
    mapped reads with deletion percentage = 3.41%
    homopolymer indels = 50.79%


>>>>>>> Coverage

     mean coverageData = 0.0043X
     std coverageData = 0.0869X

     There is a 0.35% of reference with a coverageData >= 1X
     There is a 0.06% of reference with a coverageData >= 2X
     There is a 0% of reference with a coverageData >= 3X
     There is a 0% of reference with a coverageData >= 4X
     There is a 0% of reference with a coverageData >= 5X
     There is a 0% of reference with a coverageData >= 6X
     There is a 0% of reference with a coverageData >= 7X
     There is a 0% of reference with a coverageData >= 8X
     There is a 0% of reference with a coverageData >= 9X
     There is a 0% of reference with a coverageData >= 10X
     There is a 0% of reference with a coverageData >= 11X
     There is a 0% of reference with a coverageData >= 12X
     There is a 0% of reference with a coverageData >= 13X
     There is a 0% of reference with a coverageData >= 14X
     There is a 0% of reference with a coverageData >= 15X
     There is a 0% of reference with a coverageData >= 16X
     There is a 0% of reference with a coverageData >= 17X
     There is a 0% of reference with a coverageData >= 18X
     There is a 0% of reference with a coverageData >= 19X
     There is a 0% of reference with a coverageData >= 20X
     There is a 0% of reference with a coverageData >= 21X
     There is a 0% 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

	1	249250621	1063202	0.0042655941868245135	0.11474133265687901
	2	243199373	1091086	0.004486384921724284	0.08203514966215787
	3	198022430	906302	0.0045767643594718035	0.07649298211953029
	4	191154276	899976	0.0047081133565644116	0.08801106637704532
	5	180915260	759318	0.0041970920529313	0.07387256522488687
	6	171115067	734471	0.004292263754891905	0.07515753948889856
	7	159138663	654165	0.004110660399352482	0.07727661927489896
	8	146364022	676934	0.004625002720955564	0.1183980596848048
	9	141213431	525097	0.003718463578722905	0.07655614932683714
	10	135534747	724777	0.005347536451298352	0.13105872546587533
	11	135006516	589118	0.004363626419335197	0.0819970313239365
	12	133851895	581268	0.004342620625580235	0.07449887187508934
	13	115169878	424915	0.003689462968780778	0.06887087591436021
	14	107349540	385363	0.0035897964723463184	0.0679903442535131
	15	102531392	361006	0.0035209314236170713	0.0670979108943531
	16	90354753	405846	0.004491695085481557	0.08332772067436123
	17	81195210	351366	0.004327422762993039	0.07646727778547596
	18	78077248	355035	0.004547227381784768	0.08165845973392132
	19	59128983	263166	0.004450710745354778	0.08882137386093936
	20	63025520	262814	0.00416996162824202	0.08047946626572652
	21	48129895	179259	0.0037244835044830246	0.07476818927110641
	22	51304566	150578	0.0029349824341170726	0.0611679626980567
	X	155270560	669025	0.004308769157527351	0.07526511311322369
	Y	59373566	28998	4.883991640320205E-4	0.048961688957033685
	MT	16569	56251	3.3949544329772467	2.090333991172169
	GL000207.1	4262	0	0.0	0.0
	GL000226.1	15008	21953	1.462753198294243	1.7817481720704884
	GL000229.1	19913	0	0.0	0.0
	GL000231.1	27386	1169	0.042686043964069234	0.22782437837143313
	GL000210.1	27682	0	0.0	0.0
	GL000239.1	33824	0	0.0	0.0
	GL000235.1	34474	0	0.0	0.0
	GL000201.1	36148	0	0.0	0.0
	GL000247.1	36422	0	0.0	0.0
	GL000245.1	36651	481	0.01312378925540913	0.11380490064574872
	GL000197.1	37175	0	0.0	0.0
	GL000203.1	37498	459	0.012240652834817857	0.11783916377385595
	GL000246.1	38154	0	0.0	0.0
	GL000249.1	38502	483	0.012544802867383513	0.11129883552132071
	GL000196.1	38914	0	0.0	0.0
	GL000248.1	39786	456	0.011461318051575931	0.1064422671690929
	GL000244.1	39929	0	0.0	0.0
	GL000238.1	39939	410	0.010265655124064198	0.10079817185315403
	GL000202.1	40103	423	0.01054783931376705	0.14172952867532188
	GL000234.1	40531	733	0.01808492265179739	0.16754388053836994
	GL000232.1	40652	543	0.013357276394765326	0.11943134321699386
	GL000206.1	41001	0	0.0	0.0
	GL000240.1	41933	475	0.011327594019030359	0.10560617899658505
	GL000236.1	41934	924	0.022034625840606666	0.14664074791144804
	GL000241.1	42152	930	0.022063010058834695	0.1716172805993474
	GL000243.1	43341	110	0.0025380125054797996	0.050314719496404106
	GL000242.1	43523	444	0.01020150265376927	0.10048597910840303
	GL000230.1	43691	939	0.021491840424801446	0.15435104773307612
	GL000237.1	45867	852	0.018575446399372097	0.1350199955207974
	GL000233.1	45941	0	0.0	0.0
	GL000204.1	81310	1345	0.016541630795720085	0.15485361072846573
	GL000198.1	90085	1750	0.01942609757451296	0.1441201421470368
	GL000208.1	92689	3998	0.04313348941082545	0.26966787890682825
	GL000191.1	106433	0	0.0	0.0
	GL000227.1	128374	476	0.0037079159331328774	0.06077966183326209
	GL000228.1	129120	4339	0.0336043990086741	0.31051049552382226
	GL000214.1	137718	2220	0.016119897181196358	0.13417453858876183
	GL000221.1	155397	2809	0.0180762820389068	0.1740454893979014
	GL000209.1	159169	463	0.002908857880617457	0.057412879155664565
	GL000218.1	161147	1369	0.008495348967092158	0.11158253527221668
	GL000220.1	161802	40235	0.24866812523949025	0.6522381339854945
	GL000213.1	164239	490	0.0029834570351743497	0.05453949045685721
	GL000211.1	166566	384	0.002305392457044055	0.06786361381261032
	GL000199.1	169874	21154	0.1245275910380635	0.5192099824822648
	GL000217.1	172149	2403	0.013958837983374868	0.13067907272830356
	GL000216.1	172294	13420	0.07789011805402393	0.44542525607142536
	GL000215.1	172545	960	0.005563765974093715	0.0995128835326423
	GL000205.1	174588	1778	0.010183975989185969	0.12506909205934466
	GL000219.1	179198	1205	0.006724405406310338	0.0920058264135254
	GL000224.1	179693	2523	0.014040613713388947	0.1395744382666369
	GL000223.1	180455	622	0.0034468427031669946	0.05856157983250805
	GL000195.1	182896	2173	0.011881069022832648	0.12355927053507777
	GL000212.1	186858	1274	0.006818011538173372	0.12426267041345786
	GL000222.1	186861	437	0.0023386367406789004	0.048247704382161936
	GL000200.1	187035	370	0.0019782393669634025	0.0628694305917733
	GL000193.1	189789	3642	0.019189731754738155	0.15465456173194198
	GL000194.1	191469	1260	0.006580699747739843	0.09088955242033304
	GL000225.1	211173	10094	0.04779967135950145	0.2717200747790388
	GL000192.1	547496	3452	0.006305068895480515	0.08493163306317596
	NC_007605	171823	12864	0.07486774180406582	0.29800908736364445


