BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240214.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 = 3,645,109 number of mapped reads = 2,752,194 (75.5%) number of supplementary alignments = 26,788 (0.73%) number of secondary alignments = 0 number of mapped bases = 176,727,681 bp number of sequenced bases = 176,649,611 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 502,829 duplication rate = 12.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7297 >>>>>>> ACTG content number of A's = 48,815,379 bp (27.63%) number of C's = 32,591,067 bp (18.45%) number of T's = 55,947,583 bp (31.67%) number of G's = 39,279,206 bp (22.24%) number of N's = 16,376 bp (0.01%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,495,331 number of insertions = 13,129 mapped reads with insertion percentage = 0.47% number of deletions = 44,949 mapped reads with deletion percentage = 1.61% homopolymer indels = 46.75% >>>>>>> Coverage mean coverageData = 0.0571X std coverageData = 0.6168X There is a 2.49% of reference with a coverageData >= 1X There is a 1.29% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 12329268 0.049465345163573336 0.8585950770776786 chr2 243199373 13920679 0.057239781617364614 0.7054799272830704 chr3 198022430 12785602 0.0645664332065817 0.498769010545422 chr4 191154276 10496513 0.054911212135270254 0.4844939459149947 chr5 180915260 10421865 0.05760633459001745 0.46541696884955897 chr6 171115067 9827369 0.05743134822838249 0.5405972756712892 chr7 159138663 9025159 0.056712547597562765 0.6385173376638573 chr8 146364022 8664823 0.059200498056824376 0.8993903096116174 chr9 141213431 9595495 0.06795029999660585 0.6650254226263603 chr10 135534747 9606321 0.07087718251320453 0.62085751578943 chr11 135006516 7507208 0.0556062642191285 0.5531494141841302 chr12 133851895 7537618 0.05631312130470771 0.4692132295288369 chr13 115169878 5793989 0.050308197773726915 0.44006310939538157 chr14 107349540 6159988 0.05738252814124774 0.5058749343474737 chr15 102531392 4930203 0.04808481484382851 0.4456467010328607 chr16 90354753 5300608 0.05866440695156347 0.498961469025881 chr17 81195210 4738652 0.0583612259885774 0.4854737853215742 chr18 78077248 5286840 0.06771293988230732 1.115405242325394 chr19 59128983 3042372 0.05145314269991757 0.6754097426651657 chr20 63025520 4190352 0.06648659146326757 0.5155227982094156 chr21 48129895 2556927 0.053125547022282095 0.4641021974923554 chr22 51304566 1907207 0.03717421564388636 0.36446821540497837 chrMT 16571 140070 8.452718604791503 7.27793685249736 chrX 155270560 10433089 0.06719296304463641 0.542237651576002 chrY 59373566 529464 0.008917503792849498 0.22733661965842505