BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818784.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,280,166 number of mapped reads = 2,146,230 (94.13%) number of supplementary alignments = 14,775 (0.65%) number of secondary alignments = 0 number of mapped bases = 145,740,328 bp number of sequenced bases = 145,681,835 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,022,563 duplication rate = 39.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7908 >>>>>>> ACTG content number of A's = 42,355,018 bp (29.07%) number of C's = 30,591,125 bp (21%) number of T's = 42,222,465 bp (28.98%) number of G's = 30,504,215 bp (20.94%) number of N's = 9,012 bp (0.01%) GC percentage = 41.94% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 725,543 number of insertions = 16,062 mapped reads with insertion percentage = 0.74% number of deletions = 36,374 mapped reads with deletion percentage = 1.68% homopolymer indels = 40.38% >>>>>>> Coverage mean coverageData = 0.0471X std coverageData = 0.5813X There is a 2.04% of reference with a coverageData >= 1X There is a 1.04% of reference with a coverageData >= 2X There is a 0.61% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 12037204 0.04829357676906249 0.8523427899389324 chr2 243199373 12810443 0.052674654716317874 0.9173097549101829 chr3 198022430 9911345 0.05005162798981913 0.43360353814733665 chr4 191154276 9720693 0.05085260556766201 0.49280852286080085 chr5 180915260 8986875 0.04967449954194025 0.4509228261167247 chr6 171115067 8656448 0.05058846162272782 0.48304947801033005 chr7 159138663 7876780 0.04949633138491304 0.5171769549778545 chr8 146364022 7603265 0.05194763642119646 0.504358236002235 chr9 141213431 6310381 0.04468683294013301 0.48260207993989984 chr10 135534747 6965515 0.05139283581648623 0.5789608396499093 chr11 135006516 6838698 0.0506545772946248 0.485913186382514 chr12 133851895 6721300 0.050214455312717086 0.4575475778404262 chr13 115169878 4695735 0.040772249493917154 0.3938931053791709 chr14 107349540 4526612 0.04216703676606346 0.4376552316408587 chr15 102531392 4202290 0.040985398891297604 0.40017928034874783 chr16 90354753 4261616 0.04716537712188754 0.654745936929935 chr17 81195210 3863249 0.04757976486543972 0.45024102081634354 chr18 78077248 3996923 0.05119190420236123 0.6388083206090472 chr19 59128983 2846363 0.04813820322260574 0.7366712130774778 chr20 63025520 3142733 0.049864451733202676 0.45799411292392656 chr21 48129895 1952201 0.04056108994212433 0.41141395433343153 chr22 51304566 1748721 0.03408509488219821 0.39118389613614224 chrMT 16571 198589 11.984128899885341 11.281079637542424 chrX 155270560 4527107 0.029156248293301705 0.35752986830091205 chrY 59373566 1339242 0.022556199504675196 0.9555788684671379