BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013310.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,532,807 number of mapped reads = 1,147,838 (74.88%) number of supplementary alignments = 15,327 (1%) number of secondary alignments = 0 number of mapped bases = 72,899,271 bp number of sequenced bases = 72,830,013 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,366 duplication rate = 6.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7186 >>>>>>> ACTG content number of A's = 20,142,822 bp (27.66%) number of C's = 13,263,340 bp (18.21%) number of T's = 23,309,132 bp (32%) number of G's = 16,098,665 bp (22.1%) number of N's = 16,054 bp (0.02%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 744,251 number of insertions = 5,627 mapped reads with insertion percentage = 0.49% number of deletions = 39,420 mapped reads with deletion percentage = 3.36% homopolymer indels = 41.59% >>>>>>> Coverage mean coverageData = 0.0235X std coverageData = 0.2777X There is a 1.64% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.05% 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% 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 3387140 0.01358929412657311 0.35019746688600006 chr2 243199373 9686774 0.039830587885602814 0.3728290302483351 chr3 198022430 2905253 0.014671332939404895 0.16101544047271185 chr4 191154276 8804620 0.04606028274251108 0.32052368380727475 chr5 180915260 3343828 0.018482841082615144 0.1830962438260822 chr6 171115067 2356007 0.013768553765052144 0.16485973990581435 chr7 159138663 4251095 0.02671315015383785 0.4200475621821425 chr8 146364022 3373347 0.023047651696808388 0.40603827202256626 chr9 141213431 3768269 0.02668491922698203 0.25417014512429903 chr10 135534747 2296873 0.016946746504791128 0.27813985124909735 chr11 135006516 3383598 0.025062479206559185 0.22963506227763053 chr12 133851895 2518160 0.01881303212031477 0.18664911769241746 chr13 115169878 1670398 0.014503775023535235 0.16444129068329713 chr14 107349540 1977358 0.018419808785393958 0.19103553861888636 chr15 102531392 2789647 0.02720773555868626 0.22430702360361607 chr16 90354753 4190457 0.046377825857152194 0.30649250321885857 chr17 81195210 2142643 0.026388785742410173 0.238053007927068 chr18 78077248 1348593 0.01727254782340689 0.30577416254492923 chr19 59128983 1320856 0.02233855434313829 0.3475293374316525 chr20 63025520 1263344 0.020044959565585496 0.19726161005387619 chr21 48129895 1817066 0.037753375526790575 0.27967964748695695 chr22 51304566 566997 0.011051589443325571 0.14072763464277013 chrMT 16571 11585 0.6991129080924506 1.045295050442985 chrX 155270560 3496154 0.02251652856793973 0.20735754761093333 chrY 59373566 229209 0.0038604553413551074 0.144995906745447