BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716327.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 = 2,452,107 number of mapped reads = 2,257,296 (92.06%) number of supplementary alignments = 13,219 (0.54%) number of secondary alignments = 0 number of mapped bases = 131,024,075 bp number of sequenced bases = 130,989,346 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,665 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1458 >>>>>>> ACTG content number of A's = 31,705,283 bp (24.2%) number of C's = 24,972,156 bp (19.06%) number of T's = 41,506,667 bp (31.69%) number of G's = 32,801,463 bp (25.04%) number of N's = 3,777 bp (0%) GC percentage = 44.11% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 636,184 number of insertions = 7,871 mapped reads with insertion percentage = 0.35% number of deletions = 22,181 mapped reads with deletion percentage = 0.98% homopolymer indels = 42.26% >>>>>>> Coverage mean coverageData = 0.0423X std coverageData = 0.3516X There is a 3.67% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% 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 15185220 0.060923499163518635 0.6192333193870873 chr2 243199373 10807001 0.04443679630703653 0.4363999539942971 chr3 198022430 11395601 0.05754702131470662 0.27451859022334535 chr4 191154276 5879865 0.0307597879735633 0.21104680408012386 chr5 180915260 7962825 0.0440141146744614 0.23683087549556453 chr6 171115067 10805954 0.06315021926152184 0.424533944511105 chr7 159138663 7291568 0.0458189597835191 0.4365413223806096 chr8 146364022 9043858 0.0617901713578218 0.3168642135729846 chr9 141213431 5246420 0.03715241505604378 0.3070499788832402 chr10 135534747 6416806 0.04734436107369574 0.4175921632188749 chr11 135006516 4200427 0.03111277236426129 0.2711261665954788 chr12 133851895 5605836 0.04188088633336121 0.24321243503882112 chr13 115169878 2898907 0.02517070479140388 0.17858853737818337 chr14 107349540 2776639 0.025865401938378125 0.22768227565316843 chr15 102531392 3789731 0.036961665360009936 0.21945596339657525 chr16 90354753 2719574 0.030098848258707542 0.23069985361794057 chr17 81195210 2963457 0.0364979288802874 0.2262022309998997 chr18 78077248 2432159 0.031150675290194656 0.5098230999278779 chr19 59128983 2892223 0.04891379579452601 0.4538355354418187 chr20 63025520 2189455 0.03473918184252982 0.21102361777019293 chr21 48129895 1173555 0.024383078334162166 0.20267882780473395 chr22 51304566 1549215 0.03019643514770206 0.19650427694071196 chrMT 16571 193384 11.670025948946956 6.630027455834102 chrX 155270560 5326510 0.03430470013117747 0.253650002253391 chrY 59373566 277885 0.004680281457239742 0.11094065212923697