BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819149.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 4,693,531 number of mapped reads = 4,305,939 (91.74%) number of supplementary alignments = 19,191 (0.41%) number of secondary alignments = 0 number of mapped bases = 252,682,357 bp number of sequenced bases = 252,604,059 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 631,540 duplication rate = 9.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0027 >>>>>>> ACTG content number of A's = 62,580,784 bp (24.77%) number of C's = 47,690,256 bp (18.88%) number of T's = 80,864,587 bp (32.01%) number of G's = 61,464,651 bp (24.33%) number of N's = 3,781 bp (0%) GC percentage = 43.21% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,287,660 number of insertions = 20,211 mapped reads with insertion percentage = 0.47% number of deletions = 46,295 mapped reads with deletion percentage = 1.07% homopolymer indels = 41.07% >>>>>>> Coverage mean coverageData = 0.0816X std coverageData = 0.7442X There is a 5.28% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 0.61% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 31294442 0.12555411847900672 1.6017418161428558 chr2 243199373 19088964 0.07849100828068335 0.9019988987816301 chr3 198022430 13087205 0.06608950814309268 0.3713131164885535 chr4 191154276 12547423 0.06564029464870563 0.5746007594441574 chr5 180915260 13060628 0.07219196434839162 0.39096297035519406 chr6 171115067 10249544 0.05989854768312132 0.45099376705838323 chr7 159138663 11870274 0.07459076114017622 0.8011748658664497 chr8 146364022 27793652 0.1898940164407343 0.8502767033021335 chr9 141213431 10255216 0.07262210065556725 0.5220240495804841 chr10 135534747 12669927 0.09348102446378566 0.8382960847759129 chr11 135006516 8228710 0.060950465531604416 0.5498442299178015 chr12 133851895 10985438 0.08207159114183628 0.4192474583930672 chr13 115169878 5275125 0.0458029919941393 0.31894019614266444 chr14 107349540 5673357 0.05284938342539707 0.3420964240388335 chr15 102531392 6299823 0.06144287010167579 0.3538794776610368 chr16 90354753 7413945 0.0820537354576134 0.45252345516912035 chr17 81195210 8500965 0.10469786333454892 0.5208554394330003 chr18 78077248 5642720 0.07227098987915148 1.0402061750131486 chr19 59128983 5060447 0.08558319022669475 1.0179273630394718 chr20 63025520 6885163 0.10924404907726266 0.5067404697787243 chr21 48129895 3425280 0.07116741060831319 0.5305742027087638 chr22 51304566 2013690 0.039249722919398634 0.28658819695732274 chrMT 16571 53244 3.213083096976646 3.114996057049205 chrX 155270560 14279942 0.09196812325530351 0.48638425927821244 chrY 59373566 1027233 0.01730118416670476 0.5882028165322115