BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013262.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 = 1,764,128 number of mapped reads = 1,498,576 (84.95%) number of supplementary alignments = 14,362 (0.81%) number of secondary alignments = 0 number of mapped bases = 100,271,270 bp number of sequenced bases = 100,236,238 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,649 duplication rate = 6.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0968 >>>>>>> ACTG content number of A's = 27,680,009 bp (27.61%) number of C's = 18,475,854 bp (18.43%) number of T's = 32,001,558 bp (31.93%) number of G's = 22,057,472 bp (22.01%) number of N's = 21,345 bp (0.02%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 815,760 number of insertions = 7,225 mapped reads with insertion percentage = 0.48% number of deletions = 21,148 mapped reads with deletion percentage = 1.4% homopolymer indels = 47.87% >>>>>>> Coverage mean coverageData = 0.0324X std coverageData = 0.3997X There is a 2.24% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 6563474 0.02633282907648202 0.8362172070856964 chr2 243199373 7827153 0.03218410024437028 0.5149626170145836 chr3 198022430 6096369 0.03078625487021849 0.24048398607783253 chr4 191154276 6222905 0.032554359390840934 0.25078451921156547 chr5 180915260 8877611 0.049070548277685366 0.3047536418508068 chr6 171115067 5261544 0.030748572245832682 0.27079888483860587 chr7 159138663 4140390 0.026017498965666186 0.3543167685857561 chr8 146364022 5948548 0.04064214633292873 0.4451401453075386 chr9 141213431 4148440 0.029377092324879495 0.3545387756597093 chr10 135534747 3887678 0.028683994961085514 0.3104453296220001 chr11 135006516 3958990 0.029324436459052094 0.2964339854880347 chr12 133851895 5214328 0.038955952024437156 0.27318114307478 chr13 115169878 2612696 0.022685584506740557 0.20898566474326866 chr14 107349540 2837330 0.02643076067209976 0.23065439400958088 chr15 102531392 2568915 0.025054911962962525 0.21774096347640495 chr16 90354753 3442899 0.038104237858964655 0.2732280138224427 chr17 81195210 3128419 0.03852960045303165 0.33503681878689734 chr18 78077248 3358852 0.04301960028099351 0.5301218589645743 chr19 59128983 1931245 0.032661562942829576 0.6160539480913 chr20 63025520 3091645 0.049053859452488455 0.30844106797460685 chr21 48129895 1473203 0.030608897027512735 0.24651220869031573 chr22 51304566 1290443 0.02515259557989439 0.20988967695554736 chrMT 16571 13730 0.8285559109287309 1.1166878045326147 chrX 155270560 6148862 0.03960095204139149 0.29513079400150566 chrY 59373566 225601 0.003799687557927715 0.09070305555788725