BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237262.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 = 3,793,260 number of mapped reads = 3,367,318 (88.77%) number of supplementary alignments = 39,596 (1.04%) number of secondary alignments = 0 number of mapped bases = 214,601,859 bp number of sequenced bases = 214,494,785 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 858,999 duplication rate = 18.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7657 >>>>>>> ACTG content number of A's = 57,487,342 bp (26.8%) number of C's = 37,296,328 bp (17.39%) number of T's = 71,253,340 bp (33.22%) number of G's = 48,433,340 bp (22.58%) number of N's = 24,435 bp (0.01%) GC percentage = 39.97% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,332,745 number of insertions = 17,729 mapped reads with insertion percentage = 0.52% number of deletions = 60,077 mapped reads with deletion percentage = 1.76% homopolymer indels = 43.09% >>>>>>> Coverage mean coverageData = 0.0693X std coverageData = 0.9815X There is a 3% of reference with a coverageData >= 1X There is a 1.63% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.52% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 16228766 0.06511023296507655 1.1908795638478844 chr2 243199373 17150069 0.07051855762802481 1.0906542517948767 chr3 198022430 17497218 0.08835977823320318 0.560955019257436 chr4 191154276 15756289 0.08242708104526 0.7285563115317143 chr5 180915260 15883765 0.08779671211814857 0.560241459243436 chr6 171115067 17044486 0.09960832963937652 0.6957717030412819 chr7 159138663 7776145 0.04886395834555931 0.6406766926374488 chr8 146364022 5618850 0.038389557236955404 2.8461513659598645 chr9 141213431 9356808 0.06626004292750312 0.7322383596984774 chr10 135534747 10108585 0.07458297760352185 0.937965995315703 chr11 135006516 11182080 0.08282622447645416 0.7106650446683261 chr12 133851895 5351577 0.03998133160535381 0.3945304810773525 chr13 115169878 5118881 0.044446352543674655 0.4051105619826058 chr14 107349540 9228546 0.08596726171346426 0.5735743763154869 chr15 102531392 7334665 0.07153579851915011 0.5030052317205134 chr16 90354753 5585211 0.06181424678345366 0.5368958830278997 chr17 81195210 6826985 0.08408112990901803 0.6341346088087223 chr18 78077248 7929393 0.10155830543617521 1.6171969186182429 chr19 59128983 4370203 0.07390965949811787 0.9492502454297205 chr20 63025520 4370633 0.06934703593084199 0.5278620665024323 chr21 48129895 1800419 0.03740749901906081 0.5207510118567218 chr22 51304566 3297301 0.06426915296389019 0.4648848459222982 chrMT 16571 71543 4.317361655904894 4.357747681077261 chrX 155270560 8857695 0.05704684133296099 0.49862602592982036 chrY 59373566 855746 0.014412912305115714 0.6195751109378338