BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716141.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 412,738 number of mapped reads = 367,935 (89.14%) number of supplementary alignments = 772 (0.19%) number of secondary alignments = 0 number of mapped bases = 21,091,818 bp number of sequenced bases = 21,085,134 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,974 duplication rate = 1.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1583 >>>>>>> ACTG content number of A's = 5,243,200 bp (24.87%) number of C's = 4,053,266 bp (19.22%) number of T's = 6,711,309 bp (31.83%) number of G's = 5,077,199 bp (24.08%) number of N's = 160 bp (0%) GC percentage = 43.3% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 102,424 number of insertions = 1,391 mapped reads with insertion percentage = 0.38% number of deletions = 4,117 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.94% >>>>>>> Coverage mean coverageData = 0.0068X std coverageData = 0.0948X There is a 0.65% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 2437394 0.00977888837436437 0.12120827945646415 chr2 243199373 2174444 0.00894099344573557 0.12310083538655443 chr3 198022430 1333076 0.006731944456999139 0.08434465456352253 chr4 191154276 893951 0.00467659431275291 0.07105973479302238 chr5 180915260 1515828 0.008378663027098986 0.09389356849279432 chr6 171115067 807174 0.004717141594550525 0.07362030366818176 chr7 159138663 1471160 0.009244516525817488 0.13454786460899754 chr8 146364022 924746 0.006318123725788295 0.08514827349007673 chr9 141213431 588664 0.004168611978558895 0.07334820917930887 chr10 135534747 962602 0.007102252531596197 0.10217982964612518 chr11 135006516 900774 0.006672077961037081 0.0937005490315672 chr12 133851895 823920 0.006155460107606247 0.08082638474966229 chr13 115169878 619801 0.00538162417780802 0.07541619591085796 chr14 107349540 454164 0.004230702805060925 0.0674539374629786 chr15 102531392 893515 0.008714550564182334 0.09595691180465779 chr16 90354753 616216 0.0068199621994429 0.08675136532804899 chr17 81195210 786652 0.009688404032700944 0.1033499889575989 chr18 78077248 693441 0.008881473383897958 0.12510498222163596 chr19 59128983 333886 0.005646740110513993 0.08954362760733929 chr20 63025520 563453 0.008940076971994837 0.09687716226112784 chr21 48129895 264116 0.0054875665114166566 0.0768067163468315 chr22 51304566 235678 0.004593704193891827 0.06943479895284188 chrMT 16571 2057 0.12413252066863799 0.35323614942493115 chrX 155270560 752545 0.004846668937112096 0.07557447040337682 chrY 59373566 42561 7.168341547819445E-4 0.03044092845351345