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

>>>>>>> Input

     bam file = ERR9714259.sorted.bam
     outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.result/quality.files/genome_results.txt


>>>>>>> Reference

     number of bases = 3,095,693,983 bp
     number of contigs = 25


>>>>>>> Globals

     number of windows = 424

     number of reads = 432,796
     number of mapped reads = 63,525 (14.68%)
     number of supplementary alignments = 1,151 (0.27%)
     number of secondary alignments = 0

     number of mapped bases = 6,395,746 bp
     number of sequenced bases = 6,382,328 bp
     number of aligned bases = 0 bp
     number of duplicated reads (estimated) = 62,558
     duplication rate = 32.91%


>>>>>>> Insert size

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


>>>>>>> Mapping quality

     mean mapping quality = 7.6683


>>>>>>> ACTG content

     number of A's = 156,681 bp (2.45%)
     number of C's = 64,001 bp (1%)
     number of T's = 79,223 bp (1.24%)
     number of G's = 6,082,292 bp (95.3%)
     number of N's = 131 bp (0%)

     GC percentage = 96.3%


>>>>>>> Mismatches and indels

    general error rate = 0.0315
    number of mismatches = 154,731
    number of insertions = 6,553
    mapped reads with insertion percentage = 7.25%
    number of deletions = 3,008
    mapped reads with deletion percentage = 4.55%
    homopolymer indels = 63.88%


>>>>>>> Coverage

     mean coverageData = 0.0021X
     std coverageData = 7.8782X

     There is a 0% of reference with a coverageData >= 1X
     There is a 0% 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

	chr1	249250621	55026	2.2076574886447324E-4	0.4848632558518712
	chr2	243199373	6087751	0.025031935423616408	28.09878065897201
	chr3	198022430	16973	8.57125124663908E-5	0.05684033554489695
	chr4	191154276	4862	2.5434952864983254E-5	0.010232307836435963
	chr5	180915260	3760	2.0783210880055115E-5	0.0059676567192495904
	chr6	171115067	4078	2.3831916566412004E-5	0.01222778405436798
	chr7	159138663	8160	5.127603717520236E-5	0.057043753445765254
	chr8	146364022	8808	6.017872342972373E-5	0.03634618382081802
	chr9	141213431	10321	7.308794869519175E-5	0.03959472366664266
	chr10	135534747	45768	3.3768462341247446E-4	0.6394912692978559
	chr11	135006516	4658	3.4502038405316676E-5	0.025137948558109385
	chr12	133851895	8772	6.553511999213758E-5	0.05935531807370748
	chr13	115169878	1350	1.1721814969709354E-5	0.005757681121647201
	chr14	107349540	8563	7.976745871477418E-5	0.08885694201561743
	chr15	102531392	2734	2.666500421646475E-5	0.012664100390392527
	chr16	90354753	2329	2.57761758255263E-5	0.007554757636972653
	chr17	81195210	9011	1.1097945309828006E-4	0.10461414101893755
	chr18	78077248	1996	2.5564425631395205E-5	0.0149904202401804
	chr19	59128983	4804	8.124611241833805E-5	0.021991612423326142
	chr20	63025520	1790	2.8401193675196968E-5	0.011248083082589235
	chr21	48129895	920	1.9114938854531055E-5	0.004892326890363885
	chr22	51304566	745	1.4521124688979924E-5	0.004777475101563506
	chrMT	16571	4182	0.252368595739545	1.8982018934504485
	chrX	155270560	97651	6.289086611138647E-4	0.11937378585442225
	chrY	59373566	734	1.2362403834730089E-5	0.005530447452883422