BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714228.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 175,170 number of mapped reads = 75,846 (43.3%) number of supplementary alignments = 2,892 (1.65%) number of secondary alignments = 0 number of mapped bases = 9,505,809 bp number of sequenced bases = 9,311,274 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,566 duplication rate = 42.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2938 >>>>>>> ACTG content number of A's = 2,360,014 bp (25.35%) number of C's = 1,846,759 bp (19.83%) number of T's = 2,247,318 bp (24.14%) number of G's = 2,857,071 bp (30.68%) number of N's = 112 bp (0%) GC percentage = 50.52% >>>>>>> Mismatches and indels general error rate = 0.0427 number of mismatches = 369,853 number of insertions = 9,423 mapped reads with insertion percentage = 11.76% number of deletions = 32,938 mapped reads with deletion percentage = 40.53% homopolymer indels = 29.34% >>>>>>> Coverage mean coverageData = 0.0031X std coverageData = 1.309X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 0.01% 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% 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 773780 0.003104425565302804 0.52840880271716 chr2 243199373 1829068 0.007520858205502035 4.257054857064828 chr3 198022430 511954 0.0025853333887479314 0.7455640511930592 chr4 191154276 193132 0.0010103462189880597 0.16331863337289043 chr5 180915260 595675 0.003292563601323625 0.6267477391435048 chr6 171115067 340543 0.001990140353917519 0.38093188838969944 chr7 159138663 354771 0.0022293199736132005 0.563193345173273 chr8 146364022 425931 0.0029100799102118142 0.7906070613069911 chr9 141213431 256439 0.0018159674910809298 0.3908887461789002 chr10 135534747 431916 0.003186754758910643 0.5215810309261691 chr11 135006516 456613 0.003382155273157334 0.5915210710785017 chr12 133851895 340952 0.002547233268531611 0.43869465354253284 chr13 115169878 221126 0.0019199985607347783 0.39999591832139636 chr14 107349540 301706 0.0028105010976292957 0.5488862257085332 chr15 102531392 227120 0.0022151264658535016 0.4395828373452353 chr16 90354753 184276 0.002039472123840569 0.3444175777359342 chr17 81195210 401818 0.004948789466767805 1.3009033152464196 chr18 78077248 174816 0.002239013342273539 0.35014270115635293 chr19 59128983 180698 0.0030559970902932663 0.44264383708131927 chr20 63025520 333947 0.005298599678352515 0.8952025846581697 chr21 48129895 104670 0.002174739836851919 0.4450752204553238 chr22 51304566 66744 0.0013009368405923168 0.24686458126835778 chrMT 16571 45699 2.7577695974895904 15.58261344995232 chrX 155270560 731298 0.0047098303760867485 0.4791945297066396 chrY 59373566 21117 3.556633266730181E-4 0.0921396426753755