BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524898.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 = 2,512,908 number of mapped reads = 2,302,762 (91.64%) number of supplementary alignments = 8,951 (0.36%) number of secondary alignments = 0 number of mapped bases = 133,820,224 bp number of sequenced bases = 133,779,690 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 131,168 duplication rate = 4.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1192 >>>>>>> ACTG content number of A's = 33,356,972 bp (24.93%) number of C's = 25,611,010 bp (19.14%) number of T's = 44,535,079 bp (33.29%) number of G's = 30,259,237 bp (22.62%) number of N's = 17,392 bp (0.01%) GC percentage = 41.76% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 674,511 number of insertions = 9,395 mapped reads with insertion percentage = 0.41% number of deletions = 25,742 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.77% >>>>>>> Coverage mean coverageData = 0.0432X std coverageData = 0.4185X There is a 3.73% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.07% 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 0.01% 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 10547863 0.04231830178669846 0.8699288956435285 chr2 243199373 11414531 0.046934870181593764 0.44814759801891774 chr3 198022430 7823602 0.039508665760742356 0.22507964675780107 chr4 191154276 8592917 0.04495278462931167 0.2806672037084953 chr5 180915260 8201648 0.04533419679467614 0.24442727763707073 chr6 171115067 7859135 0.045928947916667094 0.27345067260906847 chr7 159138663 7484833 0.04703340381840458 0.5612974358284631 chr8 146364022 7061305 0.04824481387919225 0.40941851516901157 chr9 141213431 5684065 0.04025158909990651 0.3596567753587563 chr10 135534747 6411001 0.0473015307285002 0.38085706248645795 chr11 135006516 6133857 0.04543378484042948 0.36782176652851806 chr12 133851895 6123819 0.04575070827349886 0.2499279207693277 chr13 115169878 4268416 0.03706191301166439 0.2190495897308577 chr14 107349540 4173171 0.03887460533133165 0.23635883310306388 chr15 102531392 3783334 0.03689927471188531 0.21623273204049764 chr16 90354753 3872710 0.042861165256021454 0.26708447533154983 chr17 81195210 3671700 0.04522064786826711 0.26278556002292475 chr18 78077248 3672369 0.047035072240251094 0.7464273930552683 chr19 59128983 2683101 0.045377086901697596 0.5744013352822598 chr20 63025520 2847899 0.04518644193653618 0.24733674096997468 chr21 48129895 1803553 0.03747261447381092 0.25397322712851866 chr22 51304566 1565892 0.03052149393486732 0.19601885008148268 chrMT 16571 40270 2.4301490555790237 2.0693955766128136 chrX 155270560 7681614 0.04947244345611943 0.3023965267062724 chrY 59373566 417619 0.007033753034136437 0.18660480453727304