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

>>>>>>> Input

     bam file = SRR1549030.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 = 7,943,815
     number of mapped reads = 6,939,508 (87.36%)
     number of secondary alignments = 0

     number of mapped bases = 274,872,979 bp
     number of sequenced bases = 274,844,992 bp
     number of aligned bases = 0 bp
     number of duplicated reads (estimated) = 276,296
     duplication rate = 3.13%


>>>>>>> Insert size

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


>>>>>>> Mapping quality

     mean mapping quality = 42.4104


>>>>>>> ACTG content

     number of A's = 79,097,683 bp (28.78%)
     number of C's = 57,564,975 bp (20.94%)
     number of T's = 79,844,267 bp (29.05%)
     number of G's = 58,335,255 bp (21.22%)
     number of N's = 2,812 bp (0%)

     GC percentage = 42.17%


>>>>>>> Mismatches and indels

    general error rate = 0.0026
    number of mismatches = 709,716
    number of insertions = 8,149
    mapped reads with insertion percentage = 0.12%
    number of deletions = 21,343
    mapped reads with deletion percentage = 0.31%
    homopolymer indels = 41.52%


>>>>>>> Coverage

     mean coverageData = 0.0888X
     std coverageData = 0.9139X

     There is a 6.76% of reference with a coverageData >= 1X
     There is a 1.5% of reference with a coverageData >= 2X
     There is a 0.37% of reference with a coverageData >= 3X
     There is a 0.1% of reference with a coverageData >= 4X
     There is a 0.03% of reference with a coverageData >= 5X
     There is a 0.01% of reference with a coverageData >= 6X
     There is a 0.01% of reference with a coverageData >= 7X
     There is a 0.01% 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	21755365	0.08728309246619691	0.8097805504768494
	chr2	243199373	22981858	0.09449801500927389	0.4860983311002064
	chr3	198022430	18749602	0.09468423349819513	0.3848099395873938
	chr4	191154276	17557932	0.09185215401616231	0.38554233642427593
	chr5	180915260	16735724	0.09250587263893605	0.384804345340297
	chr6	171115067	15815697	0.0924272612417	0.4099050571510646
	chr7	159138663	15258086	0.0958791893331415	0.7025160665761875
	chr8	146364022	14413055	0.0984740293622158	3.5467031285913215
	chr9	141213431	11496241	0.0814103936048406	0.46373258176077825
	chr10	135534747	12839463	0.0947318918889486	0.4538850585136177
	chr11	135006516	12776302	0.09463470637224651	0.5848027500724162
	chr12	133851895	12255402	0.09155942095552701	0.38567105260408735
	chr13	115169878	8903155	0.07730454485677236	0.3462445889378253
	chr14	107349540	8449106	0.07870649469014958	0.3906348447379396
	chr15	102531392	7997686	0.07800231562251686	0.3481582894835217
	chr16	90354753	7804149	0.08637231292082664	0.3895978754015287
	chr17	81195210	7274268	0.08958986620023521	0.40352130024579114
	chr18	78077248	7339593	0.09400424820301044	0.813087093219047
	chr19	59128983	5374081	0.09088742486912045	0.7174545638085366
	chr20	63025520	5661749	0.08983264239628645	0.3825342588299898
	chr21	48129895	3521447	0.07316548270051285	0.3619256278231968
	chr22	51304566	3218490	0.06273301288622148	0.3465853543267456
	chrMT	16571	20037	1.2091605817391828	1.675974790673976
	chrX	155270560	15906893	0.10244629117071517	0.450705947804191
	chrY	59373566	767598	0.012928278554129627	0.17224906279446847