BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237270.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 = 933,991 number of mapped reads = 809,855 (86.71%) number of supplementary alignments = 4,583 (0.49%) number of secondary alignments = 0 number of mapped bases = 54,145,014 bp number of sequenced bases = 54,115,172 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,709 duplication rate = 2.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4569 >>>>>>> ACTG content number of A's = 15,794,824 bp (29.19%) number of C's = 9,786,744 bp (18.09%) number of T's = 17,240,118 bp (31.86%) number of G's = 11,292,612 bp (20.87%) number of N's = 874 bp (0%) GC percentage = 38.95% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 450,848 number of insertions = 4,296 mapped reads with insertion percentage = 0.53% number of deletions = 17,106 mapped reads with deletion percentage = 2.09% homopolymer indels = 45.06% >>>>>>> Coverage mean coverageData = 0.0175X std coverageData = 0.2051X There is a 1.6% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 3445175 0.013822132062009988 0.2789478108444335 chr2 243199373 3824259 0.01572478971810507 0.19760725677441784 chr3 198022430 4788829 0.02418326550179189 0.16505004022573416 chr4 191154276 2252345 0.011782864852052799 0.12218068633200975 chr5 180915260 2891548 0.015982886131330216 0.13572661380584788 chr6 171115067 4891080 0.028583572947436593 0.20366472750783668 chr7 159138663 2767136 0.017388206912357936 0.23637931346120503 chr8 146364022 2948667 0.02014611896904555 0.4256004455913112 chr9 141213431 2761311 0.01955416691206943 0.2055670471392035 chr10 135534747 1679176 0.012389265757806004 0.17708737986135653 chr11 135006516 2581582 0.019121906678933927 0.17744758706416214 chr12 133851895 2146476 0.01603620180349333 0.1375421826932704 chr13 115169878 2193066 0.019042010272859716 0.14686425611853304 chr14 107349540 2202362 0.02051580286231315 0.15763893226006162 chr15 102531392 2002312 0.019528770271645197 0.1484341406111787 chr16 90354753 927370 0.010263654862738654 0.12353405683590375 chr17 81195210 1387141 0.017084025030540594 0.16793850733234536 chr18 78077248 1390499 0.017809272683381464 0.33865482576390343 chr19 59128983 1062139 0.01796308588632414 0.21087927501270223 chr20 63025520 871588 0.013829128264233282 0.12610199928056906 chr21 48129895 1191831 0.024762800749928916 0.17492055201350343 chr22 51304566 567757 0.011066402939652584 0.11076310534242133 chrMT 16571 32644 1.9699474986422063 1.8276735565660727 chrX 155270560 3200369 0.020611563454140953 0.1605958835761208 chrY 59373566 138352 0.0023301952252623667 0.07179321869567953