BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716711.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 = 1,254,528 number of mapped reads = 1,168,406 (93.14%) number of supplementary alignments = 26,167 (2.09%) number of secondary alignments = 0 number of mapped bases = 90,634,961 bp number of sequenced bases = 90,596,837 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,460 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0289 >>>>>>> ACTG content number of A's = 23,842,686 bp (26.32%) number of C's = 18,018,566 bp (19.89%) number of T's = 26,721,522 bp (29.49%) number of G's = 22,010,572 bp (24.3%) number of N's = 3,491 bp (0%) GC percentage = 44.18% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 603,221 number of insertions = 8,955 mapped reads with insertion percentage = 0.75% number of deletions = 18,285 mapped reads with deletion percentage = 1.54% homopolymer indels = 37.92% >>>>>>> Coverage mean coverageData = 0.0293X std coverageData = 0.2509X There is a 2.57% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.04% 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 7770679 0.031176167059579762 0.3620133605446699 chr2 243199373 7940758 0.03265122727105057 0.28872544991853616 chr3 198022430 5488508 0.027716597559175493 0.1839845088151426 chr4 191154276 6054540 0.03167357867526856 0.27023531576103615 chr5 180915260 4877325 0.02695916861850128 0.1811893832938946 chr6 171115067 5035219 0.029425924252479765 0.19732285586484158 chr7 159138663 5219141 0.032796184796399855 0.29855766594355726 chr8 146364022 4636024 0.031674614680922066 0.2556514599854911 chr9 141213431 3912327 0.027705062983704433 0.23723215102255413 chr10 135534747 4045784 0.029850529768576616 0.32959290893382903 chr11 135006516 3954128 0.029288423382468443 0.23825548408833824 chr12 133851895 4252259 0.031768388486393864 0.1982472656731741 chr13 115169878 2940818 0.02553461070784498 0.17736993535554924 chr14 107349540 2770405 0.025807329961544317 0.1871385587992032 chr15 102531392 2284204 0.022278094107997675 0.165288662665347 chr16 90354753 2884729 0.031926698975094314 0.21590519401288713 chr17 81195210 2387637 0.02940613122375076 0.20795803978464156 chr18 78077248 2508126 0.03212364759577592 0.35975136085653586 chr19 59128983 1907160 0.03225423308904197 0.2803985778322597 chr20 63025520 1996805 0.03168248354000094 0.20833906810030967 chr21 48129895 1272358 0.026435918881601548 0.22849409356723488 chr22 51304566 1279864 0.024946395609310876 0.18034636328843415 chrMT 16571 5816 0.3509745941705389 0.6534533216768236 chrX 155270560 4882082 0.03144241896210074 0.2105158700314706 chrY 59373566 328265 0.0055288072136344315 0.21485024516653245