BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008813.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 = 1,671,127 number of mapped reads = 1,447,415 (86.61%) number of supplementary alignments = 12,685 (0.76%) number of secondary alignments = 0 number of mapped bases = 96,988,477 bp number of sequenced bases = 96,953,695 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,314 duplication rate = 7.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2481 >>>>>>> ACTG content number of A's = 26,304,068 bp (27.13%) number of C's = 18,076,712 bp (18.64%) number of T's = 30,381,525 bp (31.34%) number of G's = 22,151,497 bp (22.85%) number of N's = 39,893 bp (0.04%) GC percentage = 41.49% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 753,080 number of insertions = 7,099 mapped reads with insertion percentage = 0.49% number of deletions = 19,961 mapped reads with deletion percentage = 1.36% homopolymer indels = 47.76% >>>>>>> Coverage mean coverageData = 0.0313X std coverageData = 0.3508X There is a 2.16% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 8886643 0.035653443768150134 0.6545537928753091 chr2 243199373 8104998 0.033326557959505926 0.368381252725923 chr3 198022430 6557982 0.033117369582829584 0.24774995508081046 chr4 191154276 5393340 0.028214592489680952 0.24722630288147998 chr5 180915260 5942659 0.032847748719483365 0.24732160701184397 chr6 171115067 5791171 0.033843723416828043 0.2885804463787432 chr7 159138663 5117075 0.0321548195990562 0.37583311175261563 chr8 146364022 5775303 0.03945848796092799 0.4796536280367423 chr9 141213431 3958111 0.028029281435701395 0.31004378870682603 chr10 135534747 4672641 0.03447559466060759 0.3341929230826767 chr11 135006516 4186346 0.031008473694706707 0.3228977094039026 chr12 133851895 3894961 0.029099035168684013 0.23724992113268076 chr13 115169878 2544671 0.022094935274655756 0.2038071663725052 chr14 107349540 3204865 0.02985448284175228 0.2465675942702124 chr15 102531392 2593766 0.025297286512993015 0.21432186869023062 chr16 90354753 2634774 0.029160325411990224 0.24366855603008852 chr17 81195210 2665779 0.03283172738884474 0.272387959134293 chr18 78077248 2464493 0.03156480361602909 0.5572841705781109 chr19 59128983 1833114 0.031001953813411604 0.3950607248186137 chr20 63025520 2483493 0.0394045618346346 0.2867242661623967 chr21 48129895 1317182 0.027367231945966224 0.24150538130271365 chr22 51304566 1114103 0.021715474603176646 0.19795491822586533 chrMT 16571 3741 0.225755838513065 0.5785580901784391 chrX 155270560 5543637 0.03570307854882471 0.2943937983130941 chrY 59373566 303629 0.005113875087105262 0.1331805268731116