BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716596.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,479,344 number of mapped reads = 2,122,661 (85.61%) number of supplementary alignments = 9,903 (0.4%) number of secondary alignments = 0 number of mapped bases = 122,539,293 bp number of sequenced bases = 122,504,950 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,744 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2461 >>>>>>> ACTG content number of A's = 30,336,571 bp (24.76%) number of C's = 22,193,154 bp (18.12%) number of T's = 40,101,318 bp (32.73%) number of G's = 29,872,329 bp (24.38%) number of N's = 1,578 bp (0%) GC percentage = 42.5% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 609,575 number of insertions = 8,396 mapped reads with insertion percentage = 0.39% number of deletions = 22,041 mapped reads with deletion percentage = 1.03% homopolymer indels = 42.69% >>>>>>> Coverage mean coverageData = 0.0396X std coverageData = 0.3233X There is a 3.47% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 14333317 0.057505642082231766 0.5011134604650817 chr2 243199373 10367663 0.042630303162829286 0.4736846993184105 chr3 198022430 10837392 0.05472810327597737 0.264218421020483 chr4 191154276 5631686 0.029461470168734284 0.20835401125790987 chr5 180915260 7577407 0.04188373606516112 0.23104085105442007 chr6 171115067 9013643 0.05267591660996165 0.3383680599727328 chr7 159138663 6939062 0.04360387268051887 0.42220760206958624 chr8 146364022 8607067 0.058805892885343096 0.30306929305360747 chr9 141213431 5002483 0.03542498022018883 0.28271122008497035 chr10 135534747 6121822 0.04516791550140275 0.37819329009665326 chr11 135006516 4001315 0.029637939845807145 0.2628803715484637 chr12 133851895 5354826 0.040005604702122444 0.2307795439423402 chr13 115169878 2708957 0.023521402011036252 0.1730989738070862 chr14 107349540 2644987 0.024639015686513423 0.21073129524518752 chr15 102531392 3632461 0.03542779366537811 0.21438094139161626 chr16 90354753 2618633 0.028981685114008334 0.23017822984611155 chr17 81195210 2819945 0.03473043545302734 0.21961938250152438 chr18 78077248 2321515 0.029733565916667554 0.49449973314462103 chr19 59128983 1917668 0.03243194627582213 0.37152748569881433 chr20 63025520 2107787 0.033443389281040445 0.20881145833618145 chr21 48129895 1094249 0.02273532905068669 0.19666702981105985 chr22 51304566 1488816 0.029019171509997766 0.1906956685753232 chrMT 16571 55116 3.3260515358155813 2.5942252646064508 chrX 155270560 5068805 0.03264498434217021 0.24511397653976297 chrY 59373566 272671 0.0045924645994818636 0.11245398128304042