BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234109.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 = 4,405,543 number of mapped reads = 4,061,565 (92.19%) number of supplementary alignments = 25,219 (0.57%) number of secondary alignments = 0 number of mapped bases = 262,058,026 bp number of sequenced bases = 261,952,407 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 406,883 duplication rate = 8.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5696 >>>>>>> ACTG content number of A's = 68,819,293 bp (26.27%) number of C's = 46,566,712 bp (17.78%) number of T's = 85,859,198 bp (32.78%) number of G's = 60,682,097 bp (23.17%) number of N's = 25,107 bp (0.01%) GC percentage = 40.94% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,473,757 number of insertions = 17,746 mapped reads with insertion percentage = 0.43% number of deletions = 61,309 mapped reads with deletion percentage = 1.49% homopolymer indels = 44.68% >>>>>>> Coverage mean coverageData = 0.0847X std coverageData = 0.9976X There is a 6.69% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.07% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 23673407 0.0949783270550006 2.181057835800071 chr2 243199373 17306278 0.0711608660273972 1.4131936586150524 chr3 198022430 33499617 0.16917082069945308 0.5086484579739408 chr4 191154276 8609774 0.04504096994408851 0.31977809193139467 chr5 180915260 14859908 0.08213739404846225 0.363203633219492 chr6 171115067 17427113 0.1018444097619995 0.618752182067521 chr7 159138663 17579078 0.1104639040482576 1.5327914054170175 chr8 146364022 10605001 0.0724563376647302 1.241317584680386 chr9 141213431 10788284 0.0763970107064391 0.648013818888486 chr10 135534747 14410225 0.10632125944795544 0.6743700886402257 chr11 135006516 10655953 0.07892917553697927 0.667801722727505 chr12 133851895 6929899 0.05177288674172301 0.31651005299210044 chr13 115169878 14926449 0.1296037580242987 0.48449112405761946 chr14 107349540 10288959 0.09584539440038588 0.45249121928252906 chr15 102531392 4353824 0.04246332674387177 0.32180588536363225 chr16 90354753 6776809 0.07500224144268315 0.47845768498290975 chr17 81195210 5986280 0.07372700926569437 0.40905059254578824 chr18 78077248 5269569 0.06749173587675632 1.6713626604320388 chr19 59128983 6632249 0.11216578847635515 1.179850537981694 chr20 63025520 5583217 0.08858660745678894 0.4534720145158378 chr21 48129895 5169038 0.10739765794211685 0.42683961996790115 chr22 51304566 1992948 0.038845431418326394 0.2294547207249582 chrMT 16571 211799 12.781304688914368 8.65453958658796 chrX 155270560 7962165 0.05127929595925976 0.4151817438721116 chrY 59373566 560183 0.009434888920096193 0.2091155142188745