BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714103.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 1,018,458 number of mapped reads = 86,978 (8.54%) number of supplementary alignments = 2,639 (0.26%) number of secondary alignments = 0 number of mapped bases = 8,551,692 bp number of sequenced bases = 8,530,284 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,517 duplication rate = 30.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 30.184 >>>>>>> ACTG content number of A's = 330,538 bp (3.87%) number of C's = 143,089 bp (1.68%) number of T's = 187,358 bp (2.2%) number of G's = 7,868,274 bp (92.24%) number of N's = 1,025 bp (0.01%) GC percentage = 93.92% >>>>>>> Mismatches and indels general error rate = 0.0345 number of mismatches = 210,533 number of insertions = 11,531 mapped reads with insertion percentage = 8.9% number of deletions = 4,973 mapped reads with deletion percentage = 5.49% homopolymer indels = 63.2% >>>>>>> Coverage mean coverageData = 0.0028X std coverageData = 9.5764X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 42177 1.692152253454165E-4 0.024002975238074337 chr2 243199373 7860838 0.032322608002776386 34.165199139581645 chr3 198022430 44124 2.2282324280133316E-4 0.03955863226962009 chr4 191154276 32027 1.6754529728647033E-4 0.031102132426888914 chr5 180915260 33492 1.851253454241505E-4 0.031481807102515864 chr6 171115067 39968 2.3357382082549166E-4 0.035718689068479276 chr7 159138663 41428 2.603264299135151E-4 0.16045214121096432 chr8 146364022 33353 2.2787703934509261E-4 0.04999723051646353 chr9 141213431 23700 1.6783106133863427E-4 0.033438142474021645 chr10 135534747 23775 1.754162716664827E-4 0.030014089921904834 chr11 135006516 36486 2.702536224251576E-4 0.061464825124561084 chr12 133851895 35752 2.671011867258211E-4 0.07835524160057124 chr13 115169878 23764 2.063386747704986E-4 0.05245981156302375 chr14 107349540 32287 3.0076514533737173E-4 0.19714351200523272 chr15 102531392 17852 1.7411252936076397E-4 0.03705576792400507 chr16 90354753 15194 1.681593883611192E-4 0.026215274118479834 chr17 81195210 31616 3.893825756470117E-4 0.20570486119014314 chr18 78077248 12645 1.619549910365693E-4 0.02101217722995916 chr19 59128983 17796 3.009691541625196E-4 0.04748253779995851 chr20 63025520 26156 4.150064926080737E-4 0.19076868278076958 chr21 48129895 6223 1.2929593966494213E-4 0.028039436112850053 chr22 51304566 6248 1.2178253296207593E-4 0.019381033227150415 chrMT 16571 5160 0.31138736346629653 2.5650337387632143 chrX 155270560 104127 6.706165032186398E-4 0.07616821420142704 chrY 59373566 5504 9.270118624843924E-5 0.030263072914261415