BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240192.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 = 1,956,079 number of mapped reads = 1,498,352 (76.6%) number of supplementary alignments = 8,438 (0.43%) number of secondary alignments = 0 number of mapped bases = 91,718,159 bp number of sequenced bases = 91,666,292 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 197,502 duplication rate = 10.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3506 >>>>>>> ACTG content number of A's = 24,725,906 bp (26.97%) number of C's = 15,945,991 bp (17.4%) number of T's = 30,026,447 bp (32.76%) number of G's = 20,944,170 bp (22.85%) number of N's = 23,778 bp (0.03%) GC percentage = 40.24% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 857,303 number of insertions = 6,505 mapped reads with insertion percentage = 0.43% number of deletions = 30,812 mapped reads with deletion percentage = 2.03% homopolymer indels = 48.63% >>>>>>> Coverage mean coverageData = 0.0296X std coverageData = 0.3148X There is a 1.92% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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 6856236 0.02750739786521936 0.3891571914748403 chr2 243199373 8773410 0.03607496965051797 0.37000722504135825 chr3 198022430 6808750 0.034383731176311695 0.2661900154943831 chr4 191154276 5267824 0.027557971028594724 0.24785671689994765 chr5 180915260 6970882 0.038531199634569246 0.2805515287858865 chr6 171115067 4539006 0.02652604519039811 0.2718718067761783 chr7 159138663 7013645 0.04407253943059708 0.5660045658008206 chr8 146364022 5277751 0.03605907331516211 0.40542832506224263 chr9 141213431 3588229 0.025409969679158918 0.2779281237667437 chr10 135534747 4311300 0.03180955508036622 0.28662049606290224 chr11 135006516 5386778 0.039900133412819866 0.3364946266349722 chr12 133851895 3760219 0.028092385244153622 0.24606172477667607 chr13 115169878 1904800 0.016539046780964725 0.1879977114167164 chr14 107349540 3212782 0.029928232575565764 0.257905942083277 chr15 102531392 1949605 0.019014713074411396 0.2042364728638465 chr16 90354753 2702344 0.029908155468036088 0.255596921663183 chr17 81195210 2009498 0.024748972260802086 0.24407293873129704 chr18 78077248 1954848 0.025037357874089006 0.39522671408065924 chr19 59128983 1331739 0.022522609597394903 0.3016722238526835 chr20 63025520 1622774 0.025747887522387755 0.2371443874927595 chr21 48129895 1238941 0.02574161028192561 0.23681735467929554 chr22 51304566 748014 0.014579871896782053 0.17302364989323596 chrMT 16571 56768 3.425743769235411 4.183755701922556 chrX 155270560 4224942 0.02721019361300687 0.25242498378896366 chrY 59373566 207074 0.0034876463374290166 0.0887902467501728