BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548936.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 = 7,905,395 number of mapped reads = 6,916,073 (87.49%) number of secondary alignments = 0 number of mapped bases = 272,768,667 bp number of sequenced bases = 272,740,725 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 356,870 duplication rate = 2.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 33.3492 >>>>>>> ACTG content number of A's = 77,679,604 bp (28.48%) number of C's = 58,718,625 bp (21.53%) number of T's = 78,102,152 bp (28.64%) number of G's = 58,238,055 bp (21.35%) number of N's = 2,289 bp (0%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 1,057,219 number of insertions = 11,285 mapped reads with insertion percentage = 0.16% number of deletions = 22,121 mapped reads with deletion percentage = 0.32% homopolymer indels = 36.43% >>>>>>> Coverage mean coverageData = 0.0881X std coverageData = 1.1373X There is a 7.12% of reference with a coverageData >= 1X There is a 1.11% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 21500203 0.08625937585928824 1.5393564720618604 chr2 243199373 22699789 0.09333818882830755 1.0143252419991222 chr3 198022430 17872793 0.090256406812097 0.3672204986852608 chr4 191154276 17856588 0.09341453601592464 0.414353417524191 chr5 180915260 16712129 0.09237545246321399 0.40294702805400917 chr6 171115067 15542353 0.09082983323730341 0.4357181530561406 chr7 159138663 15498429 0.09738946342662184 1.4253372790229122 chr8 146364022 14279887 0.09756418828118839 3.3494993082612377 chr9 141213431 11537089 0.08169965787461109 1.0875240257802314 chr10 135534747 12635199 0.09322479496715333 0.7916519902259566 chr11 135006516 12387454 0.09175448983514248 0.8916966153826448 chr12 133851895 12377207 0.09246941927867364 0.42778764918860224 chr13 115169878 8390248 0.07285106267109183 0.31108331073596784 chr14 107349540 8182877 0.07622647474781913 0.5608577098757412 chr15 102531392 7543071 0.07356840527435735 0.33157437941634077 chr16 90354753 7563061 0.08370407475963107 0.5196750644265171 chr17 81195210 7371566 0.0907881881209495 0.4320249020146463 chr18 78077248 7168620 0.09181445534555727 2.086115221234594 chr19 59128983 6212706 0.1050704017689599 1.626931075761634 chr20 63025520 5292220 0.0839694777607547 0.40533036391488003 chr21 48129895 3355252 0.06971243132776417 0.483494305409258 chr22 51304566 3012285 0.05871377997817972 0.3539027806032355 chrMT 16571 6279 0.3789149719389295 0.7094636116926024 chrX 155270560 16523839 0.10641965225088387 0.6579549549878873 chrY 59373566 1247523 0.021011421143207063 0.2800978045091488