BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751224.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 5,469,273 number of mapped reads = 5,224,000 (95.52%) number of supplementary alignments = 168,168 (3.07%) number of secondary alignments = 0 number of mapped bases = 514,174,822 bp number of sequenced bases = 514,023,484 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 159,799 duplication rate = 1.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.1575 >>>>>>> ACTG content number of A's = 149,646,148 bp (29.11%) number of C's = 107,500,564 bp (20.91%) number of T's = 150,141,197 bp (29.21%) number of G's = 106,732,807 bp (20.76%) number of N's = 2,768 bp (0%) GC percentage = 41.68% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 1,895,263 number of insertions = 118,918 mapped reads with insertion percentage = 2.23% number of deletions = 68,234 mapped reads with deletion percentage = 1.28% homopolymer indels = 48.02% >>>>>>> Coverage mean coverageData = 0.1661X std coverageData = 1.6407X There is a 12.91% of reference with a coverageData >= 1X There is a 2.55% of reference with a coverageData >= 2X There is a 0.57% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 63066857 0.25302587711506647 4.810080468758815 chr2 243199373 37469348 0.1540684399708547 0.6139315893388302 chr3 198022430 33618564 0.16977149507760309 0.5088023664087573 chr4 191154276 22338174 0.11685939999584419 0.4901137909985399 chr5 180915260 40996844 0.22660799315657507 0.564730151683784 chr6 171115067 29668690 0.1733844396063615 1.086768050975967 chr7 159138663 28826057 0.18113798656207133 0.7883699601688009 chr8 146364022 25022971 0.1709639476838099 0.6000212431338953 chr9 141213431 22937570 0.16243192901389103 0.7664847533780995 chr10 135534747 26119942 0.19271767999094727 1.954329813737813 chr11 135006516 23142377 0.17141674110011104 0.7925106983166793 chr12 133851895 27711600 0.20703180929937526 0.5367940432221093 chr13 115169878 14388194 0.12493018356761652 0.4112772527077277 chr14 107349540 10923302 0.1017545301079073 0.39280720564974064 chr15 102531392 12939513 0.12620050062326277 0.4150515205036944 chr16 90354753 15031254 0.16635819921946995 1.0829793138652053 chr17 81195210 15085095 0.18578799168079005 0.811361814415192 chr18 78077248 10326292 0.13225737669442447 1.544096105053221 chr19 59128983 10232171 0.17304831710026197 3.466741163571876 chr20 63025520 9634495 0.1528665689707915 0.47170525183048106 chr21 48129895 6443654 0.1338804915323418 0.48130733631937994 chr22 51304566 6234684 0.12152298491327262 0.4190569900033207 chrMT 16571 523747 31.606239816546978 15.103603548324712 chrX 155270560 20344566 0.13102655133078672 0.4971678780188341 chrY 59373566 1148861 0.019349705220670088 0.7540218828358266