BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240209.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 = 2,107,866 number of mapped reads = 1,559,757 (74%) number of supplementary alignments = 7,528 (0.36%) number of secondary alignments = 0 number of mapped bases = 94,276,474 bp number of sequenced bases = 94,228,511 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 164,026 duplication rate = 8.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9011 >>>>>>> ACTG content number of A's = 24,836,094 bp (26.36%) number of C's = 16,405,655 bp (17.41%) number of T's = 30,786,099 bp (32.67%) number of G's = 22,179,760 bp (23.54%) number of N's = 20,903 bp (0.02%) GC percentage = 40.95% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 890,622 number of insertions = 6,456 mapped reads with insertion percentage = 0.41% number of deletions = 28,289 mapped reads with deletion percentage = 1.8% homopolymer indels = 49.04% >>>>>>> Coverage mean coverageData = 0.0305X std coverageData = 0.2915X There is a 2.24% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 7071809 0.028372282370361677 0.39223640700708545 chr2 243199373 9631336 0.03960263499528019 0.3889909078184497 chr3 198022430 6576150 0.03320911676520685 0.23871410262875498 chr4 191154276 5977120 0.03126856550151146 0.23780975646704194 chr5 180915260 5530765 0.030571025351869157 0.23016298968834084 chr6 171115067 5168603 0.030205423114494062 0.2674050843968552 chr7 159138663 5462791 0.03432723950935795 0.4435024899710889 chr8 146364022 5172312 0.035338684530000136 0.33003218961508207 chr9 141213431 3597703 0.025477059614818085 0.26563605639350185 chr10 135534747 4290418 0.03165548388857065 0.2690020355185594 chr11 135006516 4248622 0.03146975513389295 0.26901757268393467 chr12 133851895 4518190 0.0337551440717369 0.2421967222750876 chr13 115169878 2308302 0.020042584398674106 0.1858692955530563 chr14 107349540 3158079 0.029418654239226363 0.23383627284286515 chr15 102531392 2576198 0.025125943867025623 0.2151684826975785 chr16 90354753 2812506 0.0311273719048294 0.23445168451901757 chr17 81195210 2503543 0.030833629225172274 0.2452292824976612 chr18 78077248 2291231 0.029345693639202038 0.37991752939672335 chr19 59128983 1819856 0.03077773213180413 0.30723909784255643 chr20 63025520 2037756 0.032332236211617134 0.24062480492673688 chr21 48129895 1457803 0.030288929572773845 0.23171548243197174 chr22 51304566 913274 0.017801027690205976 0.16974325970473608 chrMT 16571 37340 2.2533341379518435 2.785548648383796 chrX 155270560 4904996 0.03158999362145664 0.24891168152920268 chrY 59373566 209771 0.0035330705923912334 0.0796041462229971