BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230398.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 = 2,100,913 number of mapped reads = 1,916,620 (91.23%) number of supplementary alignments = 16,253 (0.77%) number of secondary alignments = 0 number of mapped bases = 131,359,567 bp number of sequenced bases = 131,287,505 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,669 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3916 >>>>>>> ACTG content number of A's = 38,825,803 bp (29.57%) number of C's = 24,117,688 bp (18.37%) number of T's = 41,605,564 bp (31.69%) number of G's = 26,670,863 bp (20.31%) number of N's = 67,587 bp (0.05%) GC percentage = 38.68% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,178,150 number of insertions = 11,360 mapped reads with insertion percentage = 0.59% number of deletions = 43,016 mapped reads with deletion percentage = 2.21% homopolymer indels = 46.31% >>>>>>> Coverage mean coverageData = 0.0424X std coverageData = 0.4065X There is a 3.54% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 9589382 0.03847285098639734 0.8135139311173682 chr2 243199373 13207057 0.05430547306550827 0.400441044142247 chr3 198022430 10969350 0.05539448233212773 0.27134106439228417 chr4 191154276 5052726 0.02643271239195298 0.2193329827102501 chr5 180915260 9019922 0.04985716517224694 0.2582180618039712 chr6 171115067 8606238 0.05029503334151165 0.32212483058917724 chr7 159138663 7665144 0.04816644714427443 0.5946718296900564 chr8 146364022 6483108 0.0442944100019334 0.5830514443355654 chr9 141213431 6170234 0.04369438484927117 0.32815574807034836 chr10 135534747 5830571 0.04301901268167048 0.4176904365640388 chr11 135006516 5454069 0.04039856120722351 0.33249830212734455 chr12 133851895 8541056 0.06380975032142802 0.29490199101138537 chr13 115169878 3087519 0.026808389950712632 0.18719498789379407 chr14 107349540 2974602 0.02770949926753296 0.20495458772602954 chr15 102531392 4003941 0.03905087916879155 0.2258210919857603 chr16 90354753 2984244 0.03302807988418716 0.23959855218961917 chr17 81195210 1663768 0.020490962459484986 0.18127777187775806 chr18 78077248 3208791 0.041097644732560244 0.555579845653845 chr19 59128983 2274786 0.038471590150637294 0.471192859342191 chr20 63025520 3250484 0.05157409252632902 0.27030073598182963 chr21 48129895 2003995 0.041637219445419524 0.2647785929924777 chr22 51304566 865153 0.016863079983953085 0.14485252672937737 chrMT 16571 6902 0.41651077183030594 0.8420298584037735 chrX 155270560 8102538 0.052183350146995024 0.28516157597546404 chrY 59373566 343987 0.0057936051878709795 0.1631680258610771