BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714087.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 = 550,642 number of mapped reads = 281,496 (51.12%) number of supplementary alignments = 4,505 (0.82%) number of secondary alignments = 0 number of mapped bases = 35,502,613 bp number of sequenced bases = 35,108,656 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 269,219 duplication rate = 35.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 32.9759 >>>>>>> ACTG content number of A's = 9,367,719 bp (26.68%) number of C's = 7,007,573 bp (19.96%) number of T's = 8,984,075 bp (25.59%) number of G's = 9,748,952 bp (27.77%) number of N's = 337 bp (0%) GC percentage = 47.73% >>>>>>> Mismatches and indels general error rate = 0.0318 number of mismatches = 988,852 number of insertions = 34,610 mapped reads with insertion percentage = 11.79% number of deletions = 90,965 mapped reads with deletion percentage = 31.19% homopolymer indels = 28.43% >>>>>>> Coverage mean coverageData = 0.0115X std coverageData = 11.5469X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 432148 0.0017337890604493219 0.5138474094707294 chr2 243199373 10342201 0.04252560716922572 20.58115635613423 chr3 198022430 2198487 0.011102212006993349 8.943070360923473 chr4 191154276 278716 0.0014580683510318126 0.49093854411612203 chr5 180915260 4123077 0.022790100735559843 21.29665012586952 chr6 171115067 1108751 0.006479563836421254 2.34852733157723 chr7 159138663 533220 0.003350662811588407 1.41313682041308 chr8 146364022 722732 0.004937907486581641 2.386090583614234 chr9 141213431 793232 0.00561725605264842 2.5168793142288175 chr10 135534747 4615083 0.034050921274084794 23.524425908120502 chr11 135006516 1807323 0.013386931635210852 6.2474135101637 chr12 133851895 166213 0.0012417680003708577 0.6121121897491562 chr13 115169878 1090631 0.009469759097947469 4.060926655834457 chr14 107349540 4782984 0.044555235169149304 33.900052628005476 chr15 102531392 163460 0.0015942434488746627 0.5461107655007426 chr16 90354753 554353 0.0061352942882816576 4.26201604993237 chr17 81195210 52787 6.501245578402963E-4 0.1570945072626917 chr18 78077248 123817 0.0015858268979972246 0.41338854058874946 chr19 59128983 12120 2.0497562083893783E-4 0.027097692939905327 chr20 63025520 47257 7.498073796138454E-4 0.25769414327862866 chr21 48129895 30656 6.369430060048957E-4 0.2002832419914941 chr22 51304566 39406 7.68079784555628E-4 0.3659370885329607 chrMT 16571 312561 18.8619274636413 151.6631950775404 chrX 155270560 1156251 0.007446685321415727 2.614291915838684 chrY 59373566 15147 2.551135298156085E-4 0.06592670696090386