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

>>>>>>> Input

     bam file = SRR2971293.sorted.bam
     outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 12,110,562
     number of mapped reads = 10,433,982 (86.16%)
     number of secondary alignments = 0

     number of mapped bases = 412,669,429 bp
     number of sequenced bases = 412,634,295 bp
     number of aligned bases = 0 bp
     number of duplicated reads (estimated) = 743,005
     duplication rate = 5.85%


>>>>>>> Insert size

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


>>>>>>> Mapping quality

     mean mapping quality = 41.905


>>>>>>> ACTG content

     number of A's = 118,940,518 bp (28.82%)
     number of C's = 85,028,850 bp (20.61%)
     number of T's = 121,085,918 bp (29.34%)
     number of G's = 87,571,802 bp (21.22%)
     number of N's = 7,207 bp (0%)

     GC percentage = 41.83%


>>>>>>> Mismatches and indels

    general error rate = 0.0026
    number of mismatches = 1,048,865
    number of insertions = 11,066
    mapped reads with insertion percentage = 0.11%
    number of deletions = 26,594
    mapped reads with deletion percentage = 0.25%
    homopolymer indels = 41.07%


>>>>>>> Coverage

     mean coverageData = 0.1333X
     std coverageData = 0.9696X

     There is a 9.57% of reference with a coverageData >= 1X
     There is a 2.43% of reference with a coverageData >= 2X
     There is a 0.7% of reference with a coverageData >= 3X
     There is a 0.23% of reference with a coverageData >= 4X
     There is a 0.09% of reference with a coverageData >= 5X
     There is a 0.04% of reference with a coverageData >= 6X
     There is a 0.02% of reference with a coverageData >= 7X
     There is a 0.01% 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% 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	32585913	0.1307355338544974	2.080880117017409
	chr2	243199373	34497649	0.14184925139589072	0.8193244610251647
	chr3	198022430	27997575	0.1413858773473288	0.497800139636304
	chr4	191154276	27439431	0.1435459963239326	0.5772825385595985
	chr5	180915260	25531185	0.1411223409235904	0.5133775989721939
	chr6	171115067	24894071	0.14548146715800309	0.6296509549833773
	chr7	159138663	22581789	0.1419000799321784	1.287688025222532
	chr8	146364022	21267937	0.14530850347908586	1.0880135597374556
	chr9	141213431	17065201	0.12084686902055372	0.7747370350582279
	chr10	135534747	19269409	0.14217320227114896	0.8532054398451666
	chr11	135006516	18888968	0.13991152841837648	0.7836907683423107
	chr12	133851895	18453605	0.13786584792094278	0.5209824722492956
	chr13	115169878	13303196	0.11550933482798341	0.43956131641402835
	chr14	107349540	14196431	0.13224491693210796	0.6270114741292312
	chr15	102531392	11578610	0.11292746322999302	0.44665833415163586
	chr16	90354753	10916295	0.12081594645054257	0.5585788405291459
	chr17	81195210	9918050	0.12215067859298596	0.5570791062660474
	chr18	78077248	11021126	0.14115669138338482	1.8336483043878413
	chr19	59128983	7288022	0.12325633945031661	1.7586788040258512
	chr20	63025520	8229751	0.13057807377075192	0.5126710547505351
	chr21	48129895	5276559	0.10963163331231036	0.5679274699555868
	chr22	51304566	4211098	0.08208037467854226	0.3702744245525118
	chrMT	16571	46529	2.80785709975258	3.340348839449545
	chrX	155270560	24766458	0.15950517599730432	0.6580496192417515
	chrY	59373566	1444571	0.024330204454958964	0.37510802444833435