BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008758.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 = 1,790,519 number of mapped reads = 1,614,642 (90.18%) number of supplementary alignments = 8,633 (0.48%) number of secondary alignments = 0 number of mapped bases = 107,859,447 bp number of sequenced bases = 107,806,637 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,753 duplication rate = 3.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.745 >>>>>>> ACTG content number of A's = 29,065,555 bp (26.96%) number of C's = 20,717,156 bp (19.22%) number of T's = 33,329,886 bp (30.92%) number of G's = 24,541,775 bp (22.76%) number of N's = 152,265 bp (0.14%) GC percentage = 41.98% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 889,923 number of insertions = 7,783 mapped reads with insertion percentage = 0.48% number of deletions = 29,187 mapped reads with deletion percentage = 1.79% homopolymer indels = 45.47% >>>>>>> Coverage mean coverageData = 0.0348X std coverageData = 0.3245X There is a 2.87% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.08% 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 8905779 0.035730217899838254 0.505203272366496 chr2 243199373 10831978 0.044539498052077624 0.4017246713707687 chr3 198022430 8373711 0.042286679342335105 0.26194957217901693 chr4 191154276 4293812 0.022462547476573322 0.1919582549086259 chr5 180915260 4345246 0.0240181287084351 0.1807860731092033 chr6 171115067 6159560 0.03599659637219439 0.24480186216434618 chr7 159138663 5808303 0.036498377518730314 0.39780395031393817 chr8 146364022 6375001 0.04355579269337105 0.3240826990852997 chr9 141213431 3480866 0.02464968080833614 0.25511245089362977 chr10 135534747 6764124 0.04990693641092642 0.5599631658842708 chr11 135006516 4838624 0.03583992938533426 0.3005030930150148 chr12 133851895 4778405 0.035699195741681504 0.22131784722274236 chr13 115169878 3043147 0.026423115599723046 0.18852434912725766 chr14 107349540 3664689 0.03413791060492667 0.22132084427615703 chr15 102531392 2670113 0.026041907243393322 0.1874260359445016 chr16 90354753 3523661 0.038998070195598894 0.3193742703280764 chr17 81195210 3493176 0.04302194673799107 0.2887747390458092 chr18 78077248 1883591 0.02412471044061389 0.4416412597939977 chr19 59128983 2306697 0.03901127472461348 0.37853661590047044 chr20 63025520 2987725 0.04740500356046249 0.25987866840703683 chr21 48129895 1199885 0.024930139573335865 0.19653502225072478 chr22 51304566 1733781 0.03379389273071719 0.21401988553401993 chrMT 16571 199220 12.022207470882867 7.0559274668920455 chrX 155270560 5866290 0.03778108354861347 0.23911397550748723 chrY 59373566 332063 0.005592775074348743 0.17943891517766333