BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063592.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,960,148 number of mapped reads = 1,423,038 (72.6%) number of supplementary alignments = 16,140 (0.82%) number of secondary alignments = 0 number of mapped bases = 93,152,525 bp number of sequenced bases = 93,110,044 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 204,539 duplication rate = 9.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8135 >>>>>>> ACTG content number of A's = 26,191,082 bp (28.13%) number of C's = 16,855,391 bp (18.1%) number of T's = 29,965,758 bp (32.18%) number of G's = 20,095,301 bp (21.58%) number of N's = 2,512 bp (0%) GC percentage = 39.68% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 859,756 number of insertions = 9,244 mapped reads with insertion percentage = 0.64% number of deletions = 25,239 mapped reads with deletion percentage = 1.75% homopolymer indels = 45.47% >>>>>>> Coverage mean coverageData = 0.0301X std coverageData = 0.9337X There is a 1.56% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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% 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 15458712 0.062020756209068786 2.7666164767333377 chr2 243199373 8649094 0.03556380056950229 0.5957045088315089 chr3 198022430 3527464 0.01781345678870823 0.23586595831412613 chr4 191154276 7975105 0.04172077741017941 0.39781061768900844 chr5 180915260 4092798 0.022622735086028675 0.2662523947364884 chr6 171115067 8483714 0.04957900054470364 0.40291254390558 chr7 159138663 3804412 0.023906270973258082 0.4803515892779417 chr8 146364022 5620933 0.03840378887647676 0.6059365785558992 chr9 141213431 5915461 0.04189021510283961 0.6279072903813953 chr10 135534747 2847501 0.021009379978405095 0.5634435163070038 chr11 135006516 4019409 0.02977196300658555 0.5396355027056206 chr12 133851895 2753418 0.020570631443058762 0.24841478775227746 chr13 115169878 1364661 0.011849113880280397 0.18147062153169213 chr14 107349540 2465166 0.022963917684230412 0.29160835923667194 chr15 102531392 1223564 0.011933554944811438 0.2191062685483853 chr16 90354753 2034041 0.022511721104478036 0.39844962941522044 chr17 81195210 1119299 0.013785283639268868 0.19756747222986237 chr18 78077248 2868786 0.036742919012719304 1.7058497594921407 chr19 59128983 2376268 0.04018787199502484 1.2753764224940944 chr20 63025520 909674 0.014433423159380518 0.21987053741921503 chr21 48129895 1570027 0.032620619679307426 0.3422761589310802 chr22 51304566 931230 0.018151016032374196 0.21208215102252265 chrMT 16571 3628 0.21893669663870619 0.6911603942140487 chrX 155270560 2754519 0.017740124077610078 0.2891653896261499 chrY 59373566 383641 0.0064614781601630596 0.20973622581901108