BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004017.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 = 1,961,974 number of mapped reads = 1,809,228 (92.21%) number of supplementary alignments = 11,126 (0.57%) number of secondary alignments = 0 number of mapped bases = 122,772,709 bp number of sequenced bases = 122,720,847 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,372 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2624 >>>>>>> ACTG content number of A's = 34,892,067 bp (28.43%) number of C's = 22,872,757 bp (18.64%) number of T's = 38,490,782 bp (31.36%) number of G's = 26,443,703 bp (21.55%) number of N's = 21,538 bp (0.02%) GC percentage = 40.19% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,033,387 number of insertions = 8,798 mapped reads with insertion percentage = 0.48% number of deletions = 29,398 mapped reads with deletion percentage = 1.61% homopolymer indels = 47.08% >>>>>>> Coverage mean coverageData = 0.0397X std coverageData = 0.3025X There is a 3.46% of reference with a coverageData >= 1X There is a 0.39% 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 8230392 0.03302054761981917 0.4723602851217962 chr2 243199373 12102304 0.04976289145284926 0.36560172678250547 chr3 198022430 9370608 0.0473209423801132 0.24056170311401515 chr4 191154276 7285615 0.038113795581533313 0.23284906022169663 chr5 180915260 9102269 0.05031233407286925 0.25062266859766724 chr6 171115067 7655971 0.04474165328760909 0.2503809211062542 chr7 159138663 6560291 0.04122374083286096 0.36051761972079494 chr8 146364022 8722014 0.05959124299002934 0.42812671092097765 chr9 141213431 4968609 0.035185102187624065 0.28754141779153447 chr10 135534747 4336148 0.03199288814107573 0.28841282329664597 chr11 135006516 4813946 0.035657138208055085 0.24016171996246422 chr12 133851895 5409445 0.04041366018762753 0.22792639049433186 chr13 115169878 3681654 0.03196716071888172 0.20558832927860637 chr14 107349540 4079226 0.03799947349564795 0.230182737527934 chr15 102531392 4450565 0.04340685241062561 0.23502902868920092 chr16 90354753 3346363 0.037035826991857305 0.23041885403763626 chr17 81195210 2376317 0.029266714132520872 0.196087586751288 chr18 78077248 3915836 0.050153355815000036 0.48985065421247787 chr19 59128983 1423696 0.024077802927880563 0.3544644659209229 chr20 63025520 2015622 0.031981045138540706 0.20542900467185404 chr21 48129895 1220025 0.025348590517390492 0.20169336045225897 chr22 51304566 791629 0.015429991162969784 0.13512535843822157 chrMT 16571 17689 1.0674672620843642 1.1937330339503882 chrX 155270560 6623634 0.04265865982579054 0.24158206647045843 chrY 59373566 272841 0.004595327826528055 0.10998856755973244