BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505954.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 12,400,331 number of mapped reads = 9,436,771 (76.1%) number of supplementary alignments = 317 (0%) number of secondary alignments = 0 number of mapped bases = 440,508,188 bp number of sequenced bases = 440,418,293 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 395,397 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0564 >>>>>>> ACTG content number of A's = 131,079,351 bp (29.76%) number of C's = 89,579,043 bp (20.34%) number of T's = 128,648,853 bp (29.21%) number of G's = 91,109,712 bp (20.69%) number of N's = 1,334 bp (0%) GC percentage = 41.03% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 2,015,766 number of insertions = 17,683 mapped reads with insertion percentage = 0.19% number of deletions = 64,643 mapped reads with deletion percentage = 0.68% homopolymer indels = 47.3% >>>>>>> Coverage mean coverageData = 0.1423X std coverageData = 1.2333X There is a 10.73% of reference with a coverageData >= 1X There is a 2.4% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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% 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 47106577 0.18899281699282106 2.9710682200008622 chr2 243199373 28152020 0.11575695962012204 0.8145122585754738 chr3 198022430 28579830 0.14432622607449067 0.50946826222362 chr4 191154276 19697647 0.10304580892556126 0.40487725635065885 chr5 180915260 25857488 0.14292596434374855 0.4854330868452723 chr6 171115067 32084062 0.1874999236624791 0.7932664686648986 chr7 159138663 29775957 0.18710699486019938 1.9358086833514794 chr8 146364022 28210684 0.19274329589002412 1.4108217389766844 chr9 141213431 12739261 0.09021281410547981 0.6693928890100971 chr10 135534747 15389716 0.11354812209152536 1.6208665884101314 chr11 135006516 24354036 0.1803915597673819 1.0304475456429198 chr12 133851895 13143266 0.09819260310061355 0.45111504049831264 chr13 115169878 13375834 0.116140037935961 0.4116662191221932 chr14 107349540 17023607 0.1585810894019667 0.5836520460333591 chr15 102531392 8097623 0.07897701223055667 0.34440499632764987 chr16 90354753 14047577 0.15547136740000828 0.7156577207329949 chr17 81195210 7032985 0.08661822538546302 0.48074223740496974 chr18 78077248 11301256 0.14474454837342626 1.4044067386196453 chr19 59128983 10960812 0.18537122480188775 1.9239966608723087 chr20 63025520 11079338 0.17579129850892147 0.5359108692637685 chr21 48129895 6886578 0.14308317107278126 0.5378524872624094 chr22 51304566 3074499 0.059926420584086024 0.3272304770751253 chrMT 16571 29845 1.801037957878221 1.708110311524973 chrX 155270560 31266636 0.20136873339028338 0.7319008227900518 chrY 59373566 1241054 0.02090246693284348 0.2524581639983266