BamQC report ----------------------------------- >>>>>>> Input bam file = SRR23117304.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP418207/SRP418207.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 = 902,652 number of mapped reads = 869,026 (96.27%) number of supplementary alignments = 4,984 (0.55%) number of secondary alignments = 0 number of mapped bases = 202,419,783 bp number of sequenced bases = 202,071,688 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 294,502 duplication rate = 27.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 53.7693 >>>>>>> ACTG content number of A's = 59,496,704 bp (29.44%) number of C's = 41,798,834 bp (20.69%) number of T's = 58,853,967 bp (29.13%) number of G's = 41,922,183 bp (20.75%) number of N's = 0 bp (0%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,051,886 number of insertions = 629,918 mapped reads with insertion percentage = 33.47% number of deletions = 275,001 mapped reads with deletion percentage = 22.46% homopolymer indels = 32.88% >>>>>>> Coverage mean coverageData = 0.0654X std coverageData = 1.1437X There is a 3.97% of reference with a coverageData >= 1X There is a 1.33% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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% 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 16845866 0.0675860542790784 3.5407458188633334 chr2 243199373 17351397 0.07134638870964523 0.42857477671128696 chr3 198022430 14032302 0.07086218465251638 0.407731616019397 chr4 191154276 13317597 0.06966936486422098 0.4958643303117871 chr5 180915260 12559484 0.0694219160948612 0.404507521045718 chr6 171115067 12126798 0.07086925898816379 0.4107238953887206 chr7 159138663 10822442 0.06800636499000874 1.5619910318124957 chr8 146364022 10237188 0.06994333621140857 0.4096723216663495 chr9 141213431 8414258 0.059585394536586254 0.3929888951079646 chr10 135534747 9720787 0.07172173346809729 0.5710811614365264 chr11 135006516 9032977 0.06690771132854062 0.40021441276197295 chr12 133851895 9090911 0.06791768618591466 0.40688304373114287 chr13 115169878 6505584 0.056486853272519746 0.35924307301798036 chr14 107349540 6367886 0.059319173608009874 0.38440964878341627 chr15 102531392 5876430 0.05731347137079735 0.3726824143857971 chr16 90354753 5860151 0.06485714149426096 0.538612326096024 chr17 81195210 5044292 0.06212548745178441 0.5057416153119435 chr18 78077248 5886037 0.07538735227962953 0.517711364556138 chr19 59128983 2930544 0.04956188744189968 0.7623563076141745 chr20 63025520 4261951 0.06762262334368681 0.46622056673824647 chr21 48129895 2801460 0.0582062354384941 0.49203476761947146 chr22 51304566 2484780 0.04843194658346783 0.3866422850200261 chrMT 16571 76724 4.630016293524832 12.704734178026094 chrX 155270560 10478853 0.06748770017960906 0.40570148860098876 chrY 59373566 293084 0.004936270797681244 0.40061350685105596