BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505976.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 5,155,603 number of mapped reads = 3,114,641 (60.41%) number of supplementary alignments = 124 (0%) number of secondary alignments = 0 number of mapped bases = 145,083,818 bp number of sequenced bases = 145,054,901 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 244,634 duplication rate = 5.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0792 >>>>>>> ACTG content number of A's = 42,831,478 bp (29.53%) number of C's = 30,077,800 bp (20.74%) number of T's = 41,985,667 bp (28.94%) number of G's = 30,159,362 bp (20.79%) number of N's = 594 bp (0%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 763,439 number of insertions = 6,934 mapped reads with insertion percentage = 0.22% number of deletions = 21,014 mapped reads with deletion percentage = 0.67% homopolymer indels = 43.4% >>>>>>> Coverage mean coverageData = 0.0469X std coverageData = 0.8518X There is a 3.6% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 12050608 0.048347353967073965 0.8100674865936303 chr2 243199373 12215796 0.05022955384017376 0.3775688435604447 chr3 198022430 10153102 0.05127248463722014 0.28397725165090126 chr4 191154276 9568462 0.05005622788160909 0.28342897856137633 chr5 180915260 9033032 0.049929630037842024 0.28714527238400034 chr6 171115067 8384072 0.04899669063040486 0.4951910161797757 chr7 159138663 8037290 0.050504948630867914 0.8011636598265302 chr8 146364022 7114467 0.048608031555733004 0.5616597895286404 chr9 141213431 5696032 0.040336333163663446 0.3151152772484442 chr10 135534747 6812154 0.050261310481510696 0.4475766128888107 chr11 135006516 6582729 0.04875860214035892 0.34546091126064354 chr12 133851895 6496406 0.04853428485267242 0.28838985656945626 chr13 115169878 4574266 0.03971755531424632 0.24861684357712915 chr14 107349540 4983943 0.0464272413277225 3.894789696150599 chr15 102531392 4044265 0.03944416359820805 0.24663037993283402 chr16 90354753 4034686 0.04465383243314273 0.2844923722821278 chr17 81195210 3644801 0.0448893598526317 0.29604542806066936 chr18 78077248 3726386 0.04772691271085784 0.5592824983878697 chr19 59128983 2644467 0.04472370174200358 0.5824912821960693 chr20 63025520 3032906 0.048121871902048564 0.5561689137977653 chr21 48129895 1802903 0.03745910935396805 0.2541807945036809 chr22 51304566 1623044 0.0316354688586587 0.22268015080553122 chrMT 16571 61379 3.704000965542212 3.1379976789515154 chrX 155270560 8347106 0.05375845878317177 0.3149948002540533 chrY 59373566 419516 0.00706570327946952 0.12514536479983132