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

>>>>>>> Input

     bam file = SRR3124804.sorted.bam
     outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 179,458
     number of mapped reads = 169,873 (94.66%)
     number of supplementary alignments = 6,738 (3.75%)
     number of secondary alignments = 0

     number of mapped bases = 22,785,771 bp
     number of sequenced bases = 22,770,341 bp
     number of aligned bases = 0 bp
     number of duplicated reads (estimated) = 71,518
     duplication rate = 1.54%


>>>>>>> Insert size

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


>>>>>>> Mapping quality

     mean mapping quality = 50.828


>>>>>>> ACTG content

     number of A's = 6,719,134 bp (29.51%)
     number of C's = 4,365,742 bp (19.17%)
     number of T's = 6,226,565 bp (27.35%)
     number of G's = 5,458,900 bp (23.97%)
     number of N's = 0 bp (0%)

     GC percentage = 43.15%


>>>>>>> Mismatches and indels

    general error rate = 0.0136
    number of mismatches = 297,188
    number of insertions = 4,848
    mapped reads with insertion percentage = 2.68%
    number of deletions = 7,215
    mapped reads with deletion percentage = 4.05%
    homopolymer indels = 38.47%


>>>>>>> Coverage

     mean coverageData = 0.0074X
     std coverageData = 7.9382X

     There is a 0.4% of reference with a coverageData >= 1X
     There is a 0.01% 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	8854491	0.03552444910458217	27.849469697449145
	chr2	243199373	1473621	0.00605931249666503	0.5751014112082588
	chr3	198022430	893038	0.0045097820484275445	0.13455258893429453
	chr4	191154276	936523	0.004899304475930216	0.31366544094656734
	chr5	180915260	853059	0.004715240715459823	0.3702500092200414
	chr6	171115067	731592	0.004275438819189428	0.06939306446478173
	chr7	159138663	779985	0.0049012916490318885	0.0795893124350328
	chr8	146364022	819262	0.005597427488020246	0.571477820589825
	chr9	141213431	715134	0.005064206675921641	0.7215294716997802
	chr10	135534747	864659	0.006379611274148023	0.36440266837872304
	chr11	135006516	586584	0.00434485695490431	0.07019510411587973
	chr12	133851895	599165	0.004476328108765288	0.21758373239320453
	chr13	115169878	430111	0.0037345789321753036	0.2355248333386965
	chr14	107349540	431732	0.004021740568240907	0.2961708038463386
	chr15	102531392	434863	0.004241266908772681	0.4487743471580656
	chr16	90354753	444934	0.00492430099388352	0.12231397620182341
	chr17	81195210	421309	0.00518884057323086	0.4057133289316616
	chr18	78077248	396105	0.0050732448971562115	0.29835764321546576
	chr19	59128983	414243	0.007005752153728063	0.9509382485500105
	chr20	63025520	311397	0.0049408081043996145	0.18859635121349871
	chr21	48129895	553925	0.011508959244560996	5.328473180133603
	chr22	51304566	136836	0.0026671310307936334	0.059693923165592445
	chrMT	16571	67206	4.055639369983706	2.887800275792825
	chrX	155270560	411783	0.002652035260257965	0.05417582425541392
	chrY	59373566	224214	0.0037763269937332047	0.14105683467582622