BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081776.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,168,977 number of mapped reads = 1,957,911 (90.27%) number of supplementary alignments = 14,128 (0.65%) number of secondary alignments = 0 number of mapped bases = 131,120,976 bp number of sequenced bases = 131,074,062 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,159 duplication rate = 2.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3779 >>>>>>> ACTG content number of A's = 36,134,075 bp (27.57%) number of C's = 24,719,652 bp (18.86%) number of T's = 40,871,275 bp (31.18%) number of G's = 29,347,547 bp (22.39%) number of N's = 1,513 bp (0%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,021,391 number of insertions = 9,655 mapped reads with insertion percentage = 0.49% number of deletions = 26,624 mapped reads with deletion percentage = 1.34% homopolymer indels = 47.39% >>>>>>> Coverage mean coverageData = 0.0424X std coverageData = 0.3509X There is a 3.68% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% 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 10273062 0.04121579299896709 0.5513023433854463 chr2 243199373 11036847 0.04538188920413047 0.42661496859049924 chr3 198022430 8903124 0.04496017951097762 0.23824071306405004 chr4 191154276 8969251 0.04692152949798518 0.2598547402656707 chr5 180915260 8282306 0.045780029832751534 0.2383999485716055 chr6 171115067 7531371 0.0440134883037506 0.2699257245261254 chr7 159138663 7104389 0.044642759126360135 0.4551537648954778 chr8 146364022 6534475 0.044645363735631695 0.49572924898869103 chr9 141213431 5466911 0.038713817526322976 0.3328001150395001 chr10 135534747 6324845 0.04666585609961702 0.3904450695431091 chr11 135006516 6275575 0.046483497137278916 0.308693198635766 chr12 133851895 6032896 0.04507142764022878 0.23876397546662143 chr13 115169878 4184507 0.03633334577292858 0.21189298994536193 chr14 107349540 3994699 0.0372120737545778 0.23146548472415682 chr15 102531392 3499517 0.03413117613774326 0.21057330896901194 chr16 90354753 3638320 0.040267057118732866 0.25614784772119376 chr17 81195210 3369031 0.04149297723350922 0.2432246885545915 chr18 78077248 3611552 0.04625613853603037 0.609342168069258 chr19 59128983 2488652 0.04208853042508781 0.45784877106607863 chr20 63025520 2462359 0.03906923735020354 0.23031772995462707 chr21 48129895 1746891 0.03629534201144632 0.23134059980730476 chr22 51304566 1401379 0.027314898249017446 0.18365050392084614 chrMT 16571 5285 0.3189306619998793 0.648336207340385 chrX 155270560 7638743 0.049196338314230335 0.2777819967275761 chrY 59373566 344989 0.00581048138493147 0.13788396870114733