BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524495.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 = 2,770,042 number of mapped reads = 2,563,071 (92.53%) number of supplementary alignments = 6,117 (0.22%) number of secondary alignments = 0 number of mapped bases = 149,364,773 bp number of sequenced bases = 149,317,263 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 161,478 duplication rate = 4.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4729 >>>>>>> ACTG content number of A's = 36,980,255 bp (24.77%) number of C's = 26,453,101 bp (17.72%) number of T's = 49,161,428 bp (32.92%) number of G's = 36,719,276 bp (24.59%) number of N's = 3,203 bp (0%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 693,636 number of insertions = 10,777 mapped reads with insertion percentage = 0.42% number of deletions = 27,555 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.39% >>>>>>> Coverage mean coverageData = 0.0482X std coverageData = 0.4124X There is a 4.01% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 14916385 0.059844926123574234 0.7861665951193862 chr2 243199373 11994883 0.04932119212330371 0.4768970201495335 chr3 198022430 8297768 0.04190317228204906 0.24067432437801722 chr4 191154276 8586652 0.04492001005512427 0.29704665407613684 chr5 180915260 8433125 0.04661367426937894 0.25380617974456654 chr6 171115067 6532376 0.03817534080736444 0.3119695859764999 chr7 159138663 7540787 0.04738500913508366 0.5731743299366626 chr8 146364022 12524114 0.08556825529159072 0.4148821809144853 chr9 141213431 5864856 0.04153185683874503 0.34115519864556004 chr10 135534747 7940598 0.05858717543479828 0.42202916552234043 chr11 135006516 5053335 0.03743030447508178 0.37596405386647674 chr12 133851895 7177729 0.05362441077132304 0.2717249873348823 chr13 115169878 3398363 0.029507394285856584 0.20195470873094315 chr14 107349540 3577349 0.0333243067459814 0.21891393752668373 chr15 102531392 3936551 0.03839361704949836 0.24499631087814489 chr16 90354753 4611570 0.05103848825750207 0.289739152199426 chr17 81195210 5374238 0.066189101549217 0.33090651445218533 chr18 78077248 3539325 0.04533106750893679 0.6509715178918137 chr19 59128983 2984212 0.05046953031476966 0.5239021240956548 chr20 63025520 4351492 0.06904333355758112 0.3165245014838625 chr21 48129895 2057257 0.04274384974245217 0.27649533025989126 chr22 51304566 1232983 0.024032617291802057 0.180855996668275 chrMT 16571 9991 0.6029207651922033 1.020140509696359 chrX 155270560 8961646 0.05771632433089698 0.32824750145282855 chrY 59373566 467188 0.007868619513269592 0.20864601070725766