BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716987.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,199,678 number of mapped reads = 2,005,694 (91.18%) number of supplementary alignments = 11,012 (0.5%) number of secondary alignments = 0 number of mapped bases = 116,808,385 bp number of sequenced bases = 116,773,504 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,467 duplication rate = 2.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0945 >>>>>>> ACTG content number of A's = 30,100,723 bp (25.78%) number of C's = 21,556,229 bp (18.46%) number of T's = 35,958,821 bp (30.79%) number of G's = 29,156,216 bp (24.97%) number of N's = 1,515 bp (0%) GC percentage = 43.43% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 586,884 number of insertions = 7,749 mapped reads with insertion percentage = 0.38% number of deletions = 22,117 mapped reads with deletion percentage = 1.1% homopolymer indels = 41.09% >>>>>>> Coverage mean coverageData = 0.0377X std coverageData = 0.3606X There is a 3.34% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9881284 0.039643969432677964 0.5228038147481051 chr2 243199373 10892803 0.04478960149292819 0.3887044343466921 chr3 198022430 8929689 0.04509433098058639 0.2539439275248156 chr4 191154276 6612926 0.034594706110576356 0.21721605845008324 chr5 180915260 5996239 0.03314390947452415 0.1999148691531905 chr6 171115067 6736828 0.03937016253513199 0.2402884762173085 chr7 159138663 7458694 0.04686915083608564 0.8770665094335116 chr8 146364022 8419480 0.05752424595164514 0.35263097369479357 chr9 141213431 4959003 0.035117077496686556 0.2474554996077708 chr10 135534747 5236268 0.03863413711909611 0.4679301807599864 chr11 135006516 3560558 0.026373230755765892 0.23110575037320624 chr12 133851895 5631164 0.04207011040075301 0.25259566411982187 chr13 115169878 3134290 0.02721449440104469 0.17993253543960686 chr14 107349540 2973190 0.027696345974095465 0.190685723518687 chr15 102531392 2838516 0.027684360317667394 0.1932383259722014 chr16 90354753 3575575 0.039572627684566854 0.23414422529889745 chr17 81195210 4850557 0.05973944768416758 0.28356479893472525 chr18 78077248 2679784 0.03432221381573285 0.3810380930953923 chr19 59128983 2316399 0.03917535669436425 0.47077927447605844 chr20 63025520 2629703 0.0417244157604729 0.23823256706834178 chr21 48129895 1225284 0.025457857325473076 0.18247821126552477 chr22 51304566 1664174 0.03243715189014561 0.19754111736593327 chrMT 16571 127185 7.675155391949792 4.786068235427246 chrX 155270560 4235993 0.027281366152089617 0.2166979938062 chrY 59373566 242799 0.004089345079930014 0.09515101091895187