BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013286.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 = 1,648,915 number of mapped reads = 1,295,209 (78.55%) number of supplementary alignments = 12,851 (0.78%) number of secondary alignments = 0 number of mapped bases = 83,549,451 bp number of sequenced bases = 83,509,894 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 199,527 duplication rate = 11.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7744 >>>>>>> ACTG content number of A's = 22,787,525 bp (27.29%) number of C's = 15,039,233 bp (18.01%) number of T's = 27,035,361 bp (32.37%) number of G's = 18,646,675 bp (22.33%) number of N's = 1,100 bp (0%) GC percentage = 40.34% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 651,150 number of insertions = 6,419 mapped reads with insertion percentage = 0.49% number of deletions = 23,017 mapped reads with deletion percentage = 1.76% homopolymer indels = 46.76% >>>>>>> Coverage mean coverageData = 0.027X std coverageData = 0.3432X There is a 1.34% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.09% 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% 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 5356023 0.02148850413496061 0.4573002649618208 chr2 243199373 9165921 0.037688917068055106 0.4423636690236507 chr3 198022430 10939729 0.05524489826733264 0.41572687262237157 chr4 191154276 4317547 0.022586714199372658 0.2859232354422562 chr5 180915260 4526464 0.025019802088557926 0.2765743037410888 chr6 171115067 3612565 0.02111190477458072 0.2758403836026589 chr7 159138663 8921922 0.056063824037531344 0.43937159516048563 chr8 146364022 2662747 0.018192633432825452 0.40717266867290774 chr9 141213431 2808481 0.019888200294488987 0.2941985910485893 chr10 135534747 2399399 0.017703201969307546 0.29187812888080855 chr11 135006516 5355112 0.03966558177088282 0.4027955382116746 chr12 133851895 4743992 0.035442098148853254 0.3370115388212879 chr13 115169878 1354679 0.011762441912111777 0.1913242571758564 chr14 107349540 2582132 0.024053498505908828 0.2790842761834017 chr15 102531392 1268127 0.012368182809807166 0.19561759077724142 chr16 90354753 2372722 0.026260068465905718 0.290824090497744 chr17 81195210 3163710 0.038964244319338544 0.35541613744918 chr18 78077248 1633901 0.020926723749279688 0.413934236303142 chr19 59128983 935084 0.01581430886440242 0.32036633223038946 chr20 63025520 1126935 0.017880614075060388 0.23742160723042235 chr21 48129895 759749 0.015785386608468604 0.23683883026347305 chr22 51304566 555108 0.010819855683020494 0.17705084468135485 chrMT 16571 19638 1.1850823728199866 1.9393177178788623 chrX 155270560 2780033 0.01790444370136876 0.2412712316106404 chrY 59373566 187731 0.0031618616271086026 0.1292831855667804