BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524315.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 = 2,151,655 number of mapped reads = 1,912,350 (88.88%) number of supplementary alignments = 10,161 (0.47%) number of secondary alignments = 0 number of mapped bases = 108,051,115 bp number of sequenced bases = 108,023,365 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,671 duplication rate = 2.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2975 >>>>>>> ACTG content number of A's = 26,740,948 bp (24.75%) number of C's = 20,002,442 bp (18.52%) number of T's = 35,065,056 bp (32.46%) number of G's = 26,199,254 bp (24.25%) number of N's = 15,665 bp (0.01%) GC percentage = 42.77% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 579,893 number of insertions = 7,359 mapped reads with insertion percentage = 0.38% number of deletions = 17,550 mapped reads with deletion percentage = 0.91% homopolymer indels = 41.33% >>>>>>> Coverage mean coverageData = 0.0349X std coverageData = 0.3395X There is a 3.12% of reference with a coverageData >= 1X There is a 0.24% 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 0.01% 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 9110634 0.03655210150910717 0.6764562897697635 chr2 243199373 7018099 0.02885738936506222 0.41638815874453383 chr3 198022430 7578831 0.03827258861534019 0.21733877401701435 chr4 191154276 5718776 0.029917070753886773 0.20975484441759604 chr5 180915260 6366190 0.035188795019281405 0.20680024516990916 chr6 171115067 6911075 0.040388465616531595 0.2472831193007902 chr7 159138663 5002961 0.0314377468409421 0.42960170319030055 chr8 146364022 11167886 0.07630212566856082 0.39821554582272584 chr9 141213431 4469851 0.03165315769432725 0.25385091697195156 chr10 135534747 5486005 0.04047674210068065 0.37042447556016184 chr11 135006516 5109174 0.03784390673410164 0.2699862068553319 chr12 133851895 4321826 0.032288119641488824 0.20113786282767337 chr13 115169878 2791049 0.024234192555105425 0.17114779752819917 chr14 107349540 2316915 0.02158290571156616 0.17826072957585798 chr15 102531392 3246822 0.031666613869828275 0.20193299166773837 chr16 90354753 3335255 0.036912889352926456 0.239425463132686 chr17 81195210 3250064 0.040027779963867326 0.2442121511450777 chr18 78077248 2560154 0.032790013295550584 0.4735011962741617 chr19 59128983 1900277 0.03213782655453418 0.45935583931456336 chr20 63025520 2383378 0.037816078312404244 0.21947218703594729 chr21 48129895 1537610 0.031947088187082064 0.20926128868826277 chr22 51304566 749172 0.014602442987238212 0.13401789117754126 chrMT 16571 138191 8.339327741234687 5.118037589174746 chrX 155270560 5274394 0.03396905376009464 0.23998585587295956 chrY 59373566 306526 0.005162667844474762 0.13997517485251262