BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080781.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,940,243 number of mapped reads = 2,601,818 (88.49%) number of supplementary alignments = 27,699 (0.94%) number of secondary alignments = 0 number of mapped bases = 173,799,366 bp number of sequenced bases = 173,740,044 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,105 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0444 >>>>>>> ACTG content number of A's = 49,326,253 bp (28.39%) number of C's = 33,592,392 bp (19.33%) number of T's = 53,027,916 bp (30.52%) number of G's = 37,789,827 bp (21.75%) number of N's = 3,656 bp (0%) GC percentage = 41.09% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,309,028 number of insertions = 13,027 mapped reads with insertion percentage = 0.5% number of deletions = 36,851 mapped reads with deletion percentage = 1.4% homopolymer indels = 47.12% >>>>>>> Coverage mean coverageData = 0.0561X std coverageData = 0.4018X There is a 4.74% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 22519064 0.09034707279625995 0.7252531523213447 chr2 243199373 13166682 0.054139457012498136 0.4586625544997134 chr3 198022430 11018956 0.05564498930752441 0.26970446324150965 chr4 191154276 9980071 0.05220950955865617 0.27151006316374143 chr5 180915260 12402978 0.06855683705177772 0.2987601385630916 chr6 171115067 12009337 0.07018281446834837 0.42840737583589267 chr7 159138663 12309270 0.0773493365342651 0.5382350956744906 chr8 146364022 7461205 0.050977042705207976 0.4934612244021696 chr9 141213431 5805182 0.04110927663814074 0.31344085277865724 chr10 135534747 6850352 0.050543142268897286 0.3920185240883748 chr11 135006516 7144179 0.05291729030323247 0.3154572751121609 chr12 133851895 6026151 0.045021036123545355 0.24435916073004793 chr13 115169878 7478068 0.06493076253844778 0.2917755356168299 chr14 107349540 3977868 0.03705528686941742 0.24076305759843136 chr15 102531392 4020152 0.03920898684375611 0.2322294126652481 chr16 90354753 4575004 0.050633794549800826 0.2801700251422867 chr17 81195210 3892156 0.047935783403971734 0.26070972047926805 chr18 78077248 2111845 0.02704814852080852 0.5712852526020491 chr19 59128983 2809054 0.047507226701328516 0.5163581199175676 chr20 63025520 3015165 0.04784038275289121 0.2613233859835465 chr21 48129895 2829452 0.05878782823025066 0.28686273892941794 chr22 51304566 846102 0.016491748512208446 0.14323395772790357 chrMT 16571 35377 2.1348741777804596 1.7413881909332887 chrX 155270560 11105542 0.07152380979369173 0.32729561371537874 chrY 59373566 410154 0.006908023681784584 0.14372887566923404