BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548917.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 = 5,651,772 number of mapped reads = 4,981,173 (88.13%) number of secondary alignments = 0 number of mapped bases = 197,627,307 bp number of sequenced bases = 197,608,190 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 147,438 duplication rate = 1.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6794 >>>>>>> ACTG content number of A's = 58,259,641 bp (29.48%) number of C's = 40,118,918 bp (20.3%) number of T's = 58,896,134 bp (29.8%) number of G's = 40,331,494 bp (20.41%) number of N's = 2,003 bp (0%) GC percentage = 40.71% >>>>>>> Mismatches and indels general error rate = 0.0025 number of mismatches = 489,406 number of insertions = 5,106 mapped reads with insertion percentage = 0.1% number of deletions = 14,455 mapped reads with deletion percentage = 0.29% homopolymer indels = 43.65% >>>>>>> Coverage mean coverageData = 0.0638X std coverageData = 0.5377X There is a 5.56% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 15373252 0.06167788845749756 0.7718868841955498 chr2 243199373 16893648 0.06946419224526537 0.43115062009317584 chr3 198022430 13611920 0.06873928372659602 0.29272078661226025 chr4 191154276 13429149 0.07025293538293645 0.30377188354613316 chr5 180915260 12601603 0.06965472674886573 0.29823552606942677 chr6 171115067 11672787 0.06821600928923459 0.3290494777371774 chr7 159138663 10998762 0.06911432955799057 0.6522846627037041 chr8 146364022 10288457 0.07029362038165363 1.4792608324054861 chr9 141213431 8344364 0.05909044161670429 0.43334136646429966 chr10 135534747 9066377 0.06689337753365932 0.3989378684514959 chr11 135006516 8934818 0.06618064271801519 0.4458805727241013 chr12 133851895 8978036 0.06707440339189819 0.29930745783810053 chr13 115169878 6546210 0.056839601757674864 0.26198482865213985 chr14 107349540 6082193 0.05665783942809629 0.31557188171191985 chr15 102531392 5487838 0.05352349063982278 0.2566659830149756 chr16 90354753 5221169 0.05778521689943638 0.30731388076453914 chr17 81195210 4754898 0.05856131168328772 0.2952933278024043 chr18 78077248 5323597 0.06818371723347626 0.8166268880249228 chr19 59128983 3423517 0.057899135522083985 0.7049645091011416 chr20 63025520 3851258 0.06110632645315739 0.28297645756449974 chr21 48129895 2554675 0.0530787569763034 0.30303393237443776 chr22 51304566 1922506 0.03747241522323764 0.21316247040168107 chrMT 16571 5562 0.33564661155029873 0.658205728046422 chrX 155270560 11666970 0.07513961436089366 0.3711224213528022 chrY 59373566 593741 0.010000089939014275 0.14281336242849021