BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238510.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 = 3,108,447 number of mapped reads = 2,541,919 (81.77%) number of supplementary alignments = 25,313 (0.81%) number of secondary alignments = 0 number of mapped bases = 152,043,525 bp number of sequenced bases = 151,962,668 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,082,480 duplication rate = 22.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6884 >>>>>>> ACTG content number of A's = 38,286,211 bp (25.19%) number of C's = 26,286,226 bp (17.3%) number of T's = 51,800,504 bp (34.09%) number of G's = 35,586,404 bp (23.42%) number of N's = 3,323 bp (0%) GC percentage = 40.72% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 927,181 number of insertions = 9,777 mapped reads with insertion percentage = 0.38% number of deletions = 48,805 mapped reads with deletion percentage = 1.9% homopolymer indels = 40.69% >>>>>>> Coverage mean coverageData = 0.0491X std coverageData = 1.048X There is a 1.27% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.28% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 7981509 0.03202202252487066 0.6512963778086058 chr2 243199373 15095132 0.062068959363641124 2.154626796940904 chr3 198022430 18715386 0.0945114449913578 0.9886835136690075 chr4 191154276 9557110 0.049996841294829314 0.6634074996524146 chr5 180915260 5735582 0.03170314101751284 0.5126847439614214 chr6 171115067 14854011 0.08680714831499906 1.3111826366879973 chr7 159138663 13252136 0.08327414438564185 1.043261614078732 chr8 146364022 5350842 0.03655845150251474 0.75250240302989 chr9 141213431 5553219 0.039325005848770855 0.6733260700722369 chr10 135534747 12296223 0.09072376842227772 1.0021969215335405 chr11 135006516 3023029 0.0223917266334019 0.4560619069791856 chr12 133851895 4298378 0.03211294094865075 0.5729581856474739 chr13 115169878 4504305 0.039110096131212364 0.8197831016331114 chr14 107349540 1862726 0.017351970022414627 0.4948284886608244 chr15 102531392 3741101 0.03648737159444788 0.6863389678217393 chr16 90354753 2104840 0.023295288074109393 0.4848568874951789 chr17 81195210 1955674 0.024086076013597354 0.440035085945964 chr18 78077248 6649932 0.08517118841073906 2.796136885160661 chr19 59128983 1590289 0.026895253720159537 0.5109768723338214 chr20 63025520 2060294 0.03268983738650629 0.5296108896586058 chr21 48129895 1526909 0.03172475236025343 0.5163139778954071 chr22 51304566 1072911 0.020912583102252535 0.40217485155487454 chrMT 16571 114732 6.923661818840142 8.67925108647311 chrX 155270560 8774912 0.056513688106747346 0.9945775739610627 chrY 59373566 372343 0.00627119145917562 0.3200513406961395