BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525267.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 973,198 number of mapped reads = 897,496 (92.22%) number of supplementary alignments = 3,906 (0.4%) number of secondary alignments = 0 number of mapped bases = 52,382,611 bp number of sequenced bases = 52,365,146 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,215 duplication rate = 1.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1866 >>>>>>> ACTG content number of A's = 13,242,752 bp (25.29%) number of C's = 10,365,050 bp (19.79%) number of T's = 16,316,309 bp (31.16%) number of G's = 12,439,948 bp (23.76%) number of N's = 1,087 bp (0%) GC percentage = 43.55% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 261,701 number of insertions = 3,789 mapped reads with insertion percentage = 0.42% number of deletions = 11,060 mapped reads with deletion percentage = 1.22% homopolymer indels = 43.36% >>>>>>> Coverage mean coverageData = 0.0169X std coverageData = 0.1927X There is a 1.58% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 4952793 0.019870734845631538 0.31486643866403996 chr2 243199373 4351347 0.01789209793727552 0.22775858640355665 chr3 198022430 3849136 0.019437878830191106 0.1473655583089708 chr4 191154276 2537470 0.013274461095497545 0.12416386442087775 chr5 180915260 2388702 0.013203430158406759 0.12097593060834144 chr6 171115067 3242833 0.01895118329936428 0.15589074986105944 chr7 159138663 3856507 0.024233626997356386 0.3453236691047436 chr8 146364022 3504174 0.023941498410039595 0.20207150024519419 chr9 141213431 1713178 0.012131834683628641 0.14080711754471298 chr10 135534747 3468315 0.02558985851797842 0.2173398428664169 chr11 135006516 2350491 0.017410204111925974 0.16919010158231654 chr12 133851895 2317450 0.01731353896782709 0.13954272275417978 chr13 115169878 1667916 0.014482224249642775 0.12663113513088806 chr14 107349540 1605417 0.014955043123612826 0.13105790554398877 chr15 102531392 1390621 0.013562880332298619 0.12315541930711475 chr16 90354753 1336535 0.014792082935581706 0.13652568024030837 chr17 81195210 854304 0.010521605892761408 0.11036042562539944 chr18 78077248 1130101 0.0144741397647622 0.27201344335855665 chr19 59128983 946075 0.016000190634092252 0.23327635380058895 chr20 63025520 904000 0.014343396135406737 0.12766656209520522 chr21 48129895 716642 0.01488974783759657 0.13107837849606724 chr22 51304566 628711 0.012254484327964103 0.11636609273862517 chrMT 16571 9424 0.5687043630438718 0.7940702975471043 chrX 155270560 2519316 0.016225329515137964 0.1427548095400149 chrY 59373566 141153 0.002377371101476371 0.06920743606357137