BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716549.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 = 2,393,308 number of mapped reads = 2,209,384 (92.32%) number of supplementary alignments = 13,089 (0.55%) number of secondary alignments = 0 number of mapped bases = 129,134,348 bp number of sequenced bases = 129,096,800 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,310 duplication rate = 2.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4974 >>>>>>> ACTG content number of A's = 31,043,319 bp (24.05%) number of C's = 27,024,070 bp (20.93%) number of T's = 40,573,093 bp (31.43%) number of G's = 30,454,500 bp (23.59%) number of N's = 1,818 bp (0%) GC percentage = 44.52% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 644,733 number of insertions = 7,545 mapped reads with insertion percentage = 0.34% number of deletions = 23,637 mapped reads with deletion percentage = 1.06% homopolymer indels = 43.53% >>>>>>> Coverage mean coverageData = 0.0417X std coverageData = 0.362X There is a 3.63% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 10624431 0.042625494602077645 0.5539843751175194 chr2 243199373 12887070 0.05298973365363076 0.467755039209519 chr3 198022430 9112643 0.046018236418975365 0.25072693607960517 chr4 191154276 7049737 0.03687982893984543 0.23586763094173188 chr5 180915260 6857789 0.037906083765404865 0.2171771636030517 chr6 171115067 7070569 0.04132055185999489 0.254581023790876 chr7 159138663 6264145 0.0393628102807424 0.7034733015837742 chr8 146364022 10651572 0.0727745237829007 0.4086629794457432 chr9 141213431 5320758 0.03767883807029659 0.26533062800931845 chr10 135534747 6088688 0.044923446826517485 0.45569754212855623 chr11 135006516 4308156 0.03191072644227039 0.25883401884777746 chr12 133851895 5968173 0.04458788573744137 0.2560917227099254 chr13 115169878 3347650 0.029067062135812977 0.1933341130660344 chr14 107349540 4105464 0.03824389000642201 0.2245594172927318 chr15 102531392 3047914 0.029726642158530336 0.1932920053310826 chr16 90354753 3921089 0.04339659918056552 0.24954905001992234 chr17 81195210 5495698 0.06768500260052286 0.30894286715902375 chr18 78077248 2905380 0.037211608687847196 0.4255494991234281 chr19 59128983 2655888 0.04491685574906641 0.49147635698311704 chr20 63025520 2923909 0.04639246133947011 0.2522893404766482 chr21 48129895 1631297 0.03389363305280429 0.21751096951939103 chr22 51304566 1993194 0.038850226313190135 0.22077947320408192 chrMT 16571 94159 5.682155572988957 3.9832201316039915 chrX 155270560 4523598 0.029133649031728874 0.22727740478775674 chrY 59373566 285377 0.004806465557416578 0.11907910110983015