BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238668.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 = 2,732,887 number of mapped reads = 1,938,837 (70.94%) number of supplementary alignments = 16,781 (0.61%) number of secondary alignments = 0 number of mapped bases = 116,980,947 bp number of sequenced bases = 116,931,056 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,011,878 duplication rate = 20.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1079 >>>>>>> ACTG content number of A's = 28,333,633 bp (24.23%) number of C's = 19,613,483 bp (16.77%) number of T's = 41,169,292 bp (35.21%) number of G's = 27,812,227 bp (23.79%) number of N's = 2,421 bp (0%) GC percentage = 40.56% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 727,066 number of insertions = 8,852 mapped reads with insertion percentage = 0.45% number of deletions = 30,593 mapped reads with deletion percentage = 1.56% homopolymer indels = 40.97% >>>>>>> Coverage mean coverageData = 0.0378X std coverageData = 1.3211X There is a 0.78% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 13883290 0.055700122006917686 1.2138976826628838 chr2 243199373 7260600 0.02985451775815228 2.3136027915360424 chr3 198022430 6223612 0.03142882349236902 0.8979801223950347 chr4 191154276 9560757 0.050015920125166334 1.0712807080127402 chr5 180915260 8986353 0.04967161421319573 1.0637266215167973 chr6 171115067 5496939 0.03212422550727225 1.1806059311987385 chr7 159138663 8741475 0.054929926111041916 1.2907134239031552 chr8 146364022 4242380 0.028985128599431354 0.9458668984505518 chr9 141213431 6023781 0.042657280949430366 1.025158309520759 chr10 135534747 3933646 0.029023155220852703 0.7961152484828771 chr11 135006516 3725516 0.02759508289214722 0.7660885234582637 chr12 133851895 8288324 0.061921603724773566 1.2850724992399494 chr13 115169878 2551198 0.022151608079327825 0.9893767994746402 chr14 107349540 2650342 0.02468889945872148 0.8274742423413108 chr15 102531392 3342224 0.03259708012156901 0.9586089169777405 chr16 90354753 2261073 0.025024394676835652 0.7953902997660912 chr17 81195210 2051736 0.025269175361452973 0.7113102445694081 chr18 78077248 6341803 0.08122472503129209 4.168624928765544 chr19 59128983 2006832 0.03393990388774317 0.8601782601248366 chr20 63025520 2336221 0.037067857591654936 0.8817705754075681 chr21 48129895 1214011 0.02522363699318272 0.7690120049473443 chr22 51304566 860901 0.016780202370291954 0.5696633082477006 chrMT 16571 95003 5.733087924687707 11.096051921130071 chrX 155270560 4327729 0.027872180019187152 0.7635747072134 chrY 59373566 575201 0.009687829765859104 0.48134650971289256