BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716921.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 = 2,364,851 number of mapped reads = 2,156,158 (91.18%) number of supplementary alignments = 14,149 (0.6%) number of secondary alignments = 0 number of mapped bases = 125,880,411 bp number of sequenced bases = 125,844,838 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,934 duplication rate = 4.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6167 >>>>>>> ACTG content number of A's = 32,607,646 bp (25.91%) number of C's = 25,428,112 bp (20.21%) number of T's = 38,460,319 bp (30.56%) number of G's = 29,347,836 bp (23.32%) number of N's = 925 bp (0%) GC percentage = 43.53% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 627,512 number of insertions = 10,142 mapped reads with insertion percentage = 0.47% number of deletions = 22,709 mapped reads with deletion percentage = 1.05% homopolymer indels = 40.72% >>>>>>> Coverage mean coverageData = 0.0407X std coverageData = 0.3376X There is a 3.42% of reference with a coverageData >= 1X There is a 0.47% 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 15055457 0.060402886619086896 0.5438056980302819 chr2 243199373 12926488 0.053151814663601124 0.45746110557335523 chr3 198022430 8058740 0.04069609690174997 0.2327382772045352 chr4 191154276 5343573 0.027954242572109662 0.2212566912808207 chr5 180915260 9101964 0.0503106482007101 0.26030816234418036 chr6 171115067 4761287 0.02782505996388968 0.21732146694630106 chr7 159138663 8581245 0.0539230683369509 0.5626486765008148 chr8 146364022 5590469 0.03819565029444189 0.31385105327143825 chr9 141213431 3497589 0.02476810438803091 0.25859407787868116 chr10 135534747 5743254 0.0423747719837482 0.2936892355481519 chr11 135006516 5455650 0.0404102717531056 0.32373730519246036 chr12 133851895 4804294 0.03589261100860769 0.22118631695336863 chr13 115169878 3650273 0.03169468495920435 0.2061107518828947 chr14 107349540 1979202 0.018436986315917142 0.17146788861364826 chr15 102531392 5531041 0.053944854274484054 0.26989287213497065 chr16 90354753 3759246 0.04160540397913544 0.2484467823286161 chr17 81195210 4812526 0.059271057984824474 0.30835565629637296 chr18 78077248 4123707 0.052815731927436785 0.5568163289815624 chr19 59128983 1603144 0.027112659793252322 0.39194564614945576 chr20 63025520 3349890 0.05315132663720982 0.2705641098773606 chr21 48129895 1620275 0.03366462777448403 0.22718381182561034 chr22 51304566 1437704 0.028022924899121063 0.19280338343424155 chrMT 16571 2735 0.1650473719147909 0.43402420474894077 chrX 155270560 4800761 0.030918681558178188 0.23506599709697373 chrY 59373566 289897 0.004882593711821183 0.12104110773855974