BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237258.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 = 2,730,294 number of mapped reads = 2,473,798 (90.61%) number of supplementary alignments = 23,280 (0.85%) number of secondary alignments = 0 number of mapped bases = 151,735,532 bp number of sequenced bases = 151,653,870 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 580,269 duplication rate = 18.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8841 >>>>>>> ACTG content number of A's = 38,210,767 bp (25.2%) number of C's = 26,764,797 bp (17.65%) number of T's = 49,965,359 bp (32.95%) number of G's = 36,697,530 bp (24.2%) number of N's = 15,417 bp (0.01%) GC percentage = 41.85% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 1,031,870 number of insertions = 11,960 mapped reads with insertion percentage = 0.48% number of deletions = 46,088 mapped reads with deletion percentage = 1.84% homopolymer indels = 42.9% >>>>>>> Coverage mean coverageData = 0.049X std coverageData = 0.5817X There is a 2.7% of reference with a coverageData >= 1X There is a 1.12% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 15336865 0.06153190286334332 0.7414611992478939 chr2 243199373 11972795 0.04923036952073063 1.0238943645261103 chr3 198022430 12464429 0.06294453108165575 0.40456589605121746 chr4 191154276 8617721 0.0450825436936603 0.5341807361459804 chr5 180915260 8369525 0.046262128468322686 0.352547166507081 chr6 171115067 10564386 0.06173849086007137 0.5252448091008706 chr7 159138663 8812140 0.05537397282268232 0.6104383064124883 chr8 146364022 7280053 0.04973936149417922 0.9315170843393441 chr9 141213431 6444857 0.04563912196142306 0.40604262170331495 chr10 135534747 6516585 0.048080548672880176 0.6967186794076776 chr11 135006516 6758513 0.050060642998890514 0.44281113385125215 chr12 133851895 6361003 0.047522696634216495 0.3659793017959142 chr13 115169878 4507946 0.03914171030032697 0.3459090679478693 chr14 107349540 3496954 0.0325753980874068 0.30817716423094105 chr15 102531392 3805884 0.03711920735456318 0.3379992562900662 chr16 90354753 3848156 0.042589414194956626 0.3718637504158536 chr17 81195210 4340369 0.05345597357282529 0.4210486710088173 chr18 78077248 4048590 0.05185364627605727 0.7391746501017309 chr19 59128983 2736196 0.04627503909546356 0.5320713129677507 chr20 63025520 2836375 0.045003595368987036 0.3827066377674193 chr21 48129895 2669853 0.05547182265824598 0.46210638802204856 chr22 51304566 1350835 0.026329722777500935 0.256550629404135 chrMT 16571 11642 0.7025526522237644 1.4744968985867064 chrX 155270560 7978097 0.05138190394882327 0.39329711473185885 chrY 59373566 605763 0.01020257061871608 0.4087092143562562