BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084798.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,030,303 number of mapped reads = 1,837,815 (90.52%) number of supplementary alignments = 18,083 (0.89%) number of secondary alignments = 0 number of mapped bases = 122,534,320 bp number of sequenced bases = 122,487,389 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,179 duplication rate = 3.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2294 >>>>>>> ACTG content number of A's = 32,957,805 bp (26.91%) number of C's = 23,149,645 bp (18.9%) number of T's = 38,196,641 bp (31.18%) number of G's = 28,166,002 bp (23%) number of N's = 17,296 bp (0.01%) GC percentage = 41.89% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 951,980 number of insertions = 9,679 mapped reads with insertion percentage = 0.52% number of deletions = 28,422 mapped reads with deletion percentage = 1.53% homopolymer indels = 48.17% >>>>>>> Coverage mean coverageData = 0.0396X std coverageData = 0.3023X There is a 3.33% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 10011373 0.04016588989762236 0.3905994158784692 chr2 243199373 11044045 0.04541148631990922 0.5195377667164851 chr3 198022430 9092632 0.0459171822101163 0.24845783946959357 chr4 191154276 6765905 0.03539499686630081 0.22000286342039393 chr5 180915260 6040831 0.03339038951164208 0.21405311589648757 chr6 171115067 6012503 0.03513719221463999 0.23654863920731206 chr7 159138663 6709740 0.042162852656365477 0.27777166034691847 chr8 146364022 7029089 0.048024705142360735 0.30514403343765606 chr9 141213431 8460935 0.05991593674967079 0.3725492872081092 chr10 135534747 3762799 0.02776261499938462 0.21216651855760363 chr11 135006516 4897527 0.036276226845228715 0.26717181686811414 chr12 133851895 4833084 0.03610769948382128 0.22050724315978032 chr13 115169878 3071797 0.02667187856185799 0.1881238426775509 chr14 107349540 2740980 0.025533225386899654 0.19182627301903823 chr15 102531392 3128894 0.03051644905006264 0.2108442835662649 chr16 90354753 2347308 0.025978799366536923 0.19484599673894643 chr17 81195210 3998488 0.04924536804572585 0.26428877454454375 chr18 78077248 5062144 0.06483507205581836 0.5220676182019404 chr19 59128983 2982234 0.05043607802285387 0.3502822303528655 chr20 63025520 2915413 0.04625765880233912 0.2526297311729091 chr21 48129895 1188723 0.024698225499972522 0.190053747870531 chr22 51304566 1300006 0.02533899224486179 0.18163685556613932 chrMT 16571 9105 0.5494538651861686 0.8879748530552177 chrX 155270560 8845121 0.05696586010896077 0.2939640878453027 chrY 59373566 283644 0.004777277484057468 0.09912743447004453