BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240260.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 = 1,941,339 number of mapped reads = 1,551,140 (79.9%) number of supplementary alignments = 11,374 (0.59%) number of secondary alignments = 0 number of mapped bases = 95,693,355 bp number of sequenced bases = 95,648,650 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 221,140 duplication rate = 11.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8826 >>>>>>> ACTG content number of A's = 26,328,196 bp (27.53%) number of C's = 17,147,261 bp (17.93%) number of T's = 30,667,471 bp (32.06%) number of G's = 21,483,202 bp (22.46%) number of N's = 22,520 bp (0.02%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 840,362 number of insertions = 6,933 mapped reads with insertion percentage = 0.44% number of deletions = 26,438 mapped reads with deletion percentage = 1.69% homopolymer indels = 47.88% >>>>>>> Coverage mean coverageData = 0.0309X std coverageData = 0.3385X There is a 1.86% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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% 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 6403934 0.025692750430499428 0.4166927882287773 chr2 243199373 8977436 0.03691389451073955 0.4194781419054147 chr3 198022430 7399591 0.03736743862803825 0.2944325255302427 chr4 191154276 7131397 0.03730702315024331 0.2985251617695382 chr5 180915260 6597074 0.03646499471631083 0.2922963027159267 chr6 171115067 4681959 0.02736146548684693 0.27952278086860993 chr7 159138663 4968807 0.03122312897652031 0.35049247405659184 chr8 146364022 4550500 0.031090290754650075 0.6186605459120398 chr9 141213431 3478710 0.024634413138789894 0.2975419183706325 chr10 135534747 4559107 0.03363792017112778 0.30327335431457947 chr11 135006516 6575403 0.04870433809283694 0.36530332608516486 chr12 133851895 4228615 0.031591745488549115 0.2778410904627444 chr13 115169878 2175507 0.01888954853282036 0.2094559919511863 chr14 107349540 3289870 0.03064633532663484 0.28225373333723686 chr15 102531392 2239804 0.021845056000019975 0.23679610345771282 chr16 90354753 2876253 0.03183289096036818 0.27177684384278034 chr17 81195210 2383276 0.02935242115883437 0.3111789038136219 chr18 78077248 2009702 0.025739918497127357 0.4011442388063671 chr19 59128983 1589144 0.026875889274131436 0.32177709328545634 chr20 63025520 2222129 0.03525760675992836 0.2902886039262889 chr21 48129895 1352610 0.028103323308725274 0.257870294440151 chr22 51304566 923502 0.018000386164459516 0.1963441097438077 chrMT 16571 54417 3.2838694104157864 3.515436873648832 chrX 155270560 4797847 0.030899914317305224 0.2848831764324745 chrY 59373566 226761 0.0038192248718899586 0.08939448364975257