BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053605.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 8,816,345 number of mapped reads = 5,183,336 (58.79%) number of supplementary alignments = 133 (0%) number of secondary alignments = 0 number of mapped bases = 242,653,601 bp number of sequenced bases = 242,602,808 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,209,594 duplication rate = 17.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6514 >>>>>>> ACTG content number of A's = 73,249,645 bp (30.19%) number of C's = 45,170,961 bp (18.62%) number of T's = 73,734,282 bp (30.39%) number of G's = 50,345,721 bp (20.75%) number of N's = 102,199 bp (0.04%) GC percentage = 39.37% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 2,559,507 number of insertions = 13,381 mapped reads with insertion percentage = 0.26% number of deletions = 36,463 mapped reads with deletion percentage = 0.7% homopolymer indels = 46.03% >>>>>>> Coverage mean coverageData = 0.0784X std coverageData = 0.6212X There is a 3.84% of reference with a coverageData >= 1X There is a 1.58% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% 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 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 19243467 0.07720529209834948 0.6519121547960315 chr2 243199373 20782744 0.08545558215727801 0.8122074005251312 chr3 198022430 16893158 0.08530931571741646 0.5942730841350258 chr4 191154276 16195273 0.08472357165580748 0.6189299980360241 chr5 180915260 15334781 0.08476223067086767 0.5860662849411233 chr6 171115067 14635239 0.08552864021027441 0.6445291267228205 chr7 159138663 13049918 0.0820034412379096 0.6942118513936966 chr8 146364022 12431799 0.08493753335092144 0.6357823241058663 chr9 141213431 9918020 0.07023425413408446 0.5559873649609277 chr10 135534747 11140386 0.0821957929356669 0.6352776188174832 chr11 135006516 10927702 0.0809420339385693 0.6175175189453416 chr12 133851895 11122159 0.08309302606436764 0.5864300041957825 chr13 115169878 8048649 0.06988501802528609 0.5293489089032286 chr14 107349540 7451597 0.06941433563665014 0.5652451071853779 chr15 102531392 6928880 0.06757813255866067 0.5143342919736643 chr16 90354753 6566516 0.07267482652517461 0.5536138229074798 chr17 81195210 5924699 0.07296857782620428 0.5317024746752609 chr18 78077248 6405631 0.08204222310704394 0.6786817586867689 chr19 59128983 4001279 0.06767035042696405 0.5799660849208286 chr20 63025520 4900427 0.0777530593956226 0.5699229017555438 chr21 48129895 3072353 0.06383460840710332 0.5421154965601671 chr22 51304566 2461655 0.04798120697483339 0.43105703310764815 chrMT 16571 11033 0.6658017017681491 1.8306745602952266 chrX 155270560 14566074 0.09381091946857151 0.6818445547906944 chrY 59373566 640162 0.010781936190256788 0.22277182029135978