BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549052.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 = 3,940,125 number of mapped reads = 3,153,124 (80.03%) number of secondary alignments = 0 number of mapped bases = 124,535,044 bp number of sequenced bases = 124,524,219 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 111,229 duplication rate = 2.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.17 >>>>>>> ACTG content number of A's = 34,375,844 bp (27.61%) number of C's = 27,366,492 bp (21.98%) number of T's = 35,285,492 bp (28.34%) number of G's = 27,495,352 bp (22.08%) number of N's = 1,039 bp (0%) GC percentage = 44.06% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 377,346 number of insertions = 4,350 mapped reads with insertion percentage = 0.14% number of deletions = 8,530 mapped reads with deletion percentage = 0.27% homopolymer indels = 38.62% >>>>>>> Coverage mean coverageData = 0.0402X std coverageData = 0.3976X There is a 3.54% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 10085261 0.04046233048302014 0.6120101541070322 chr2 243199373 10590625 0.04354709006589421 0.41084945407929924 chr3 198022430 8361717 0.04222611044617521 0.23008216215207133 chr4 191154276 8134559 0.04255494132917016 0.25210124954679985 chr5 180915260 7683818 0.04247191751541578 0.23274968331137422 chr6 171115067 7222117 0.04220620151468018 0.23772437895760487 chr7 159138663 7154219 0.04495588227984547 0.5291507597185632 chr8 146364022 6514174 0.04450666161660958 0.7985653794364702 chr9 141213431 5342076 0.03782980104774878 0.42097882565346106 chr10 135534747 5934767 0.043787789709748746 0.3416300637501321 chr11 135006516 5767757 0.042722063874309595 0.295778735434317 chr12 133851895 5775981 0.04315203008519229 0.23934658992665495 chr13 115169878 3933696 0.03415559752524874 0.2068656839707314 chr14 107349540 3853285 0.03589475092301281 0.27254371122093024 chr15 102531392 3555541 0.034677584402638365 0.20792331597753816 chr16 90354753 3583007 0.03965488124349142 0.25464522487251434 chr17 81195210 3498120 0.04308283702942575 0.24036701452951192 chr18 78077248 3312403 0.04242468945626772 0.7020690562838122 chr19 59128983 2851630 0.048227279674335 0.6486051425026391 chr20 63025520 2586824 0.04104407230594845 0.23682772957412562 chr21 48129895 1583367 0.03289778629269813 0.2635427190104835 chr22 51304566 1497884 0.029195919910910074 0.2609094977895988 chrMT 16571 7289 0.4398648240902782 0.8066626073014312 chrX 155270560 4512744 0.029063745245718184 0.25100412856744303 chrY 59373566 1192183 0.020079356527111746 0.23193525803740156