BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714086.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 = 803,272 number of mapped reads = 59,401 (7.39%) number of supplementary alignments = 1,495 (0.19%) number of secondary alignments = 0 number of mapped bases = 5,569,831 bp number of sequenced bases = 5,501,762 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,308 duplication rate = 38.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 30.9491 >>>>>>> ACTG content number of A's = 783,252 bp (14.24%) number of C's = 531,869 bp (9.67%) number of T's = 695,001 bp (12.63%) number of G's = 3,491,078 bp (63.45%) number of N's = 562 bp (0.01%) GC percentage = 73.12% >>>>>>> Mismatches and indels general error rate = 0.0343 number of mismatches = 163,904 number of insertions = 5,053 mapped reads with insertion percentage = 6.54% number of deletions = 9,349 mapped reads with deletion percentage = 15.1% homopolymer indels = 36.74% >>>>>>> Coverage mean coverageData = 0.0018X std coverageData = 3.5456X There is a 0.01% of reference with a coverageData >= 1X There is a 0% 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 127149 5.101251081737526E-4 0.14098474181338638 chr2 243199373 3177168 0.013064046838640493 12.616473958077806 chr3 198022430 153591 7.756242563026825E-4 0.20512526098795456 chr4 191154276 84670 4.429406538622238E-4 0.20052164100898978 chr5 180915260 114039 6.303448365826078E-4 0.1764773656386323 chr6 171115067 98731 5.769860114071662E-4 0.17543677630323698 chr7 159138663 62576 3.9321682625924787E-4 0.2530296148737858 chr8 146364022 150955 0.0010313668477899575 0.37268592590369076 chr9 141213431 115906 8.207859491778795E-4 0.24104017790758214 chr10 135534747 62790 4.6327603356207986E-4 0.12901834323500497 chr11 135006516 66754 4.944502086106718E-4 0.12450472516406995 chr12 133851895 99683 7.447261019352771E-4 0.2710026898415351 chr13 115169878 51628 4.4827693574529966E-4 0.15938548744810752 chr14 107349540 75177 7.003010911830642E-4 0.3278683347700833 chr15 102531392 49101 4.788874806264212E-4 0.13230319610015917 chr16 90354753 45549 5.041129380321586E-4 0.2089488992178783 chr17 81195210 49568 6.104793620214788E-4 0.15020601501916012 chr18 78077248 39528 5.062678438666281E-4 0.13890197205454693 chr19 59128983 8367 1.4150420953460335E-4 0.04525327940307774 chr20 63025520 38802 6.156553726173144E-4 0.15378985307000048 chr21 48129895 6952 1.4444245099641293E-4 0.049755953147792194 chr22 51304566 2764 5.3874347168242294E-5 0.01041194191975013 chrMT 16571 10657 0.6431114597791322 5.872747662432602 chrX 155270560 867444 0.005586661115925646 0.7820402003294046 chrY 59373566 10282 1.7317470875843975E-4 0.05461235884529429