BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549113.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 12,847,870 number of mapped reads = 7,553,416 (58.79%) number of secondary alignments = 0 number of mapped bases = 298,093,209 bp number of sequenced bases = 298,057,824 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 548,396 duplication rate = 5.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.8196 >>>>>>> ACTG content number of A's = 81,783,020 bp (27.44%) number of C's = 67,327,136 bp (22.59%) number of T's = 82,026,689 bp (27.52%) number of G's = 66,909,198 bp (22.45%) number of N's = 11,781 bp (0%) GC percentage = 45.04% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 1,110,475 number of insertions = 10,546 mapped reads with insertion percentage = 0.14% number of deletions = 28,400 mapped reads with deletion percentage = 0.38% homopolymer indels = 44.17% >>>>>>> Coverage mean coverageData = 0.0963X std coverageData = 0.781X There is a 6.23% of reference with a coverageData >= 1X There is a 1.87% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 24946451 0.1000858128253169 0.922878154579666 chr2 243199373 24079017 0.09900937121248253 0.5990647889038516 chr3 198022430 18405451 0.092946294013259 0.45116872593594765 chr4 191154276 16571270 0.08669055355057817 0.48395104612410533 chr5 180915260 16706653 0.09234518414864507 0.4639380550986862 chr6 171115067 16678264 0.09746812067694775 0.4791108952361393 chr7 159138663 16714580 0.1050315472362615 0.6758294081121365 chr8 146364022 14503538 0.09909223456567762 2.382632550086461 chr9 141213431 13164522 0.09322429110868356 0.5624142314485636 chr10 135534747 14684584 0.10834553002116867 0.6252896034268167 chr11 135006516 13879206 0.10280397132831721 0.529436206829835 chr12 133851895 13615323 0.10171931447066924 0.4929224246263099 chr13 115169878 8398287 0.07292086390852998 0.4025509667179689 chr14 107349540 9246756 0.08613689448506254 0.6222991382112941 chr15 102531392 9536907 0.09301450818106517 0.4495433430259101 chr16 90354753 10944030 0.12112290318584569 0.5474602190864885 chr17 81195210 11101061 0.13672063906232892 0.5594854321527077 chr18 78077248 7259132 0.09297371751627312 0.9633362792705579 chr19 59128983 9206182 0.15569660651866785 1.0023089573753905 chr20 63025520 7592618 0.12046894654736684 0.5463851261762941 chr21 48129895 4028511 0.08370080591283234 0.5197746423177942 chr22 51304566 5542608 0.10803342532904381 0.5155346176115554 chrMT 16571 206142 12.439925170478547 15.438261028933649 chrX 155270560 8727661 0.05620937414021048 0.3992769130718798 chrY 59373566 2354455 0.039654936676702224 0.42652069617902216