BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081159.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 = 2,534,492 number of mapped reads = 2,285,006 (90.16%) number of supplementary alignments = 23,585 (0.93%) number of secondary alignments = 0 number of mapped bases = 154,522,872 bp number of sequenced bases = 154,462,039 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,872 duplication rate = 3.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2229 >>>>>>> ACTG content number of A's = 44,169,397 bp (28.6%) number of C's = 28,527,381 bp (18.47%) number of T's = 48,640,463 bp (31.49%) number of G's = 33,078,809 bp (21.42%) number of N's = 45,989 bp (0.03%) GC percentage = 39.88% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,302,635 number of insertions = 11,969 mapped reads with insertion percentage = 0.52% number of deletions = 37,789 mapped reads with deletion percentage = 1.64% homopolymer indels = 47.12% >>>>>>> Coverage mean coverageData = 0.0499X std coverageData = 0.4156X There is a 4.31% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.07% 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 11426310 0.04584265408911459 0.7370835956015575 chr2 243199373 13547567 0.05570560003047376 0.4669282233075917 chr3 198022430 10551581 0.05328477688108362 0.25705068271621434 chr4 191154276 10424162 0.05453271680932735 0.2705984462137058 chr5 180915260 9613837 0.05314000046209479 0.25778562374581393 chr6 171115067 9499841 0.05551726780435998 0.3531511718466551 chr7 159138663 8720649 0.054799059107339614 0.48307099476363163 chr8 146364022 8234162 0.056258101461573666 0.6033558690533464 chr9 141213431 5978862 0.0423391879770983 0.3605901320478708 chr10 135534747 7368750 0.054367976943949285 0.3539910202761553 chr11 135006516 7020933 0.0520044010320213 0.42764712443931685 chr12 133851895 6511518 0.0486471857570638 0.2513022081301506 chr13 115169878 5077552 0.04408750003190939 0.2342630908040705 chr14 107349540 5242060 0.04883169504033273 0.2694304646489388 chr15 102531392 4008363 0.03909400742359959 0.22245836334125893 chr16 90354753 4383510 0.04851443730912529 0.2813280039338258 chr17 81195210 3632679 0.04474006533144012 0.29920631525119684 chr18 78077248 4312600 0.05523504107111972 0.7756974674483161 chr19 59128983 2665793 0.045084370891344434 0.5770935831694518 chr20 63025520 2616264 0.04151118467566789 0.2359962585115984 chr21 48129895 2103865 0.04371222916650867 0.25777989450280253 chr22 51304566 1450798 0.02827814584768147 0.1854059766324087 chrMT 16571 27897 1.6834831935308672 1.5485901853146666 chrX 155270560 9713909 0.06256117708340847 0.3282807137440313 chrY 59373566 389410 0.006558642612101149 0.14116942441333763