BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714183.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 = 2,139,164 number of mapped reads = 2,009,319 (93.93%) number of supplementary alignments = 118,662 (5.55%) number of secondary alignments = 0 number of mapped bases = 256,920,701 bp number of sequenced bases = 251,222,918 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,914,084 duplication rate = 46.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.9368 >>>>>>> ACTG content number of A's = 74,004,110 bp (29.46%) number of C's = 51,550,582 bp (20.52%) number of T's = 69,413,258 bp (27.63%) number of G's = 56,253,009 bp (22.39%) number of N's = 1,959 bp (0%) GC percentage = 42.91% >>>>>>> Mismatches and indels general error rate = 0.0405 number of mismatches = 9,556,487 number of insertions = 244,607 mapped reads with insertion percentage = 11.82% number of deletions = 809,798 mapped reads with deletion percentage = 38.43% homopolymer indels = 25.54% >>>>>>> Coverage mean coverageData = 0.083X std coverageData = 15.5395X There is a 0.11% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 17236215 0.06915214466005282 15.192555049668758 chr2 243199373 22580678 0.09284842194062728 19.09461845326183 chr3 198022430 12690250 0.06408491199709043 6.669093069736412 chr4 191154276 13170259 0.0688985843037066 8.726028879302604 chr5 180915260 15927774 0.08803996965209016 19.383581373172344 chr6 171115067 20926712 0.12229613888997863 33.215377171778115 chr7 159138663 13933249 0.0875541413842342 15.696134043125785 chr8 146364022 10581902 0.07229851882589015 7.928956623537089 chr9 141213431 8994863 0.06369693687281064 8.488911170915523 chr10 135534747 11050507 0.08153264933604074 16.430097445547666 chr11 135006516 11211635 0.08304513983606539 13.827160751434448 chr12 133851895 10017609 0.07484099496686245 10.344148766912925 chr13 115169878 6629873 0.057566033021238416 7.471560996557707 chr14 107349540 7251150 0.06754709894425258 12.867925540938945 chr15 102531392 8584991 0.08373036620823406 19.3669265976541 chr16 90354753 3512002 0.038869034371661663 4.727250571115773 chr17 81195210 2712148 0.03340280787499657 5.169752994095797 chr18 78077248 7125129 0.09125743007745354 12.011545899267867 chr19 59128983 1430701 0.02419627274834069 3.4524734765562957 chr20 63025520 3049640 0.04838738339644005 5.082364087905177 chr21 48129895 3679151 0.07644211565389869 15.30750100739033 chr22 51304566 1180345 0.02300662673961612 3.0678686681952914 chrMT 16571 12615 0.7612696880091726 6.287609162835225 chrX 155270560 41638387 0.2681666569631745 24.351436762696395 chrY 59373566 1792916 0.030197209310284648 5.223926157572676