BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004115.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 = 4,484,939 number of mapped reads = 3,973,710 (88.6%) number of supplementary alignments = 28,008 (0.62%) number of secondary alignments = 0 number of mapped bases = 273,211,164 bp number of sequenced bases = 273,096,930 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 230,763 duplication rate = 4.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3845 >>>>>>> ACTG content number of A's = 76,893,562 bp (28.16%) number of C's = 51,620,921 bp (18.9%) number of T's = 86,546,426 bp (31.69%) number of G's = 57,998,095 bp (21.24%) number of N's = 37,926 bp (0.01%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 2,540,338 number of insertions = 22,893 mapped reads with insertion percentage = 0.57% number of deletions = 68,359 mapped reads with deletion percentage = 1.7% homopolymer indels = 47.68% >>>>>>> Coverage mean coverageData = 0.0883X std coverageData = 0.7467X There is a 6.31% of reference with a coverageData >= 1X There is a 1.66% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.15% 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 0.01% 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 32032648 0.1285158202273847 1.7204639656070044 chr2 243199373 25118834 0.10328494555781606 0.776662876553133 chr3 198022430 24141602 0.1219134721253547 0.47385836827479527 chr4 191154276 16685537 0.08728832725667095 0.41318128455623954 chr5 180915260 13954532 0.07713297374693544 0.3664438384466433 chr6 171115067 17536897 0.10248598973461524 0.4449018076110362 chr7 159138663 8607342 0.05408705739849027 0.44245116104559645 chr8 146364022 7176955 0.04903496707681345 0.7986191534383664 chr9 141213431 10539728 0.07463686651732157 0.6127885097973964 chr10 135534747 11851856 0.08744514792210444 0.8964057943661494 chr11 135006516 6787088 0.050272299449605824 0.4254664977394755 chr12 133851895 20763088 0.15511986587862653 0.5287181624622924 chr13 115169878 6346014 0.055101334743100104 0.3038418811920535 chr14 107349540 12742619 0.11870212951075523 0.4952602505970945 chr15 102531392 1197150 0.011675936283006868 0.14162504205404336 chr16 90354753 9590134 0.10613867761887413 0.5520316672963999 chr17 81195210 9670524 0.11910214900608053 0.480180831209709 chr18 78077248 4494898 0.05756988258602557 1.352815703222695 chr19 59128983 4723730 0.07988857173477852 1.0379295308205927 chr20 63025520 5893050 0.0935026002165472 0.4166221885122069 chr21 48129895 3661199 0.07606912502094593 0.4052087736760024 chr22 51304566 4046976 0.07888140014672378 0.3613686419342838 chrMT 16571 31402 1.894997284412528 1.9170799508373713 chrX 155270560 14912982 0.09604513566512544 0.4642656734935261 chrY 59373566 704379 0.01186351178569938 0.2444731370895556