BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237288.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 = 2,050,779 number of mapped reads = 1,899,976 (92.65%) number of supplementary alignments = 18,360 (0.9%) number of secondary alignments = 0 number of mapped bases = 118,116,366 bp number of sequenced bases = 118,041,607 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 333,537 duplication rate = 14.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0306 >>>>>>> ACTG content number of A's = 30,034,344 bp (25.44%) number of C's = 20,434,077 bp (17.31%) number of T's = 39,311,320 bp (33.3%) number of G's = 28,249,367 bp (23.93%) number of N's = 12,499 bp (0.01%) GC percentage = 41.24% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 775,472 number of insertions = 9,326 mapped reads with insertion percentage = 0.49% number of deletions = 42,924 mapped reads with deletion percentage = 2.23% homopolymer indels = 42.3% >>>>>>> Coverage mean coverageData = 0.0382X std coverageData = 0.472X There is a 2.52% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 10851576 0.043536806273393396 0.5764919265573718 chr2 243199373 8708168 0.03580670415626441 0.8118014476241577 chr3 198022430 7167695 0.036196379369751196 0.2660066178111866 chr4 191154276 6157410 0.03221173038263606 0.37816194567132805 chr5 180915260 5857902 0.03237925866507889 0.2539282122863851 chr6 171115067 10316054 0.06028723350235429 0.43867352155620626 chr7 159138663 7001950 0.0439990500611407 0.5168297171897455 chr8 146364022 7185922 0.049096232132784655 0.8702029969862135 chr9 141213431 5206845 0.03687216550952579 0.37422347185115246 chr10 135534747 6712739 0.04952780854049183 0.5614994109355269 chr11 135006516 5010058 0.03710974957682783 0.31345134809327807 chr12 133851895 4508461 0.03368245925842141 0.26743479849129576 chr13 115169878 3138220 0.0272486179068454 0.2548466445427244 chr14 107349540 3158591 0.029423423705401998 0.25244932234533907 chr15 102531392 3104847 0.030281916000906337 0.2583117539961184 chr16 90354753 3325770 0.03680791424442276 0.2982450009596053 chr17 81195210 3194685 0.03934573234061468 0.3174552353455695 chr18 78077248 2967950 0.03801299451538046 0.71398690249183 chr19 59128983 2106741 0.035629582873089496 0.43427269168743005 chr20 63025520 2803230 0.04447769728833653 0.3147841791302161 chr21 48129895 2214150 0.04600363246169559 0.3506770008726062 chr22 51304566 1230604 0.02398624715001 0.21159581904010588 chrMT 16571 13689 0.8260817090097158 1.138014578799127 chrX 155270560 5747387 0.03701530412461963 0.29850413452251523 chrY 59373566 425722 0.007170227909167524 0.2921730342589557