BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080763.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 5,422,520 number of mapped reads = 3,869,331 (71.36%) number of supplementary alignments = 30,461 (0.56%) number of secondary alignments = 0 number of mapped bases = 246,376,571 bp number of sequenced bases = 246,290,973 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 440,382 duplication rate = 9.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7061 >>>>>>> ACTG content number of A's = 72,198,676 bp (29.31%) number of C's = 50,653,378 bp (20.57%) number of T's = 69,489,984 bp (28.21%) number of G's = 53,871,719 bp (21.87%) number of N's = 77,216 bp (0.03%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 2,124,102 number of insertions = 18,623 mapped reads with insertion percentage = 0.48% number of deletions = 46,525 mapped reads with deletion percentage = 1.19% homopolymer indels = 43.54% >>>>>>> Coverage mean coverageData = 0.0796X std coverageData = 0.5714X There is a 5.39% of reference with a coverageData >= 1X There is a 1.53% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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% 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 31606950 0.1268079087353608 0.9632939179355722 chr2 243199373 18277636 0.07515494704832154 0.5007067306341492 chr3 198022430 14779308 0.07463451488803566 0.3795604125545277 chr4 191154276 14583565 0.07629212019301101 0.44610454143615214 chr5 180915260 13623167 0.07530137037638505 0.38037038592569417 chr6 171115067 16815537 0.09827034693560913 0.6439577445505338 chr7 159138663 16569897 0.10412238413741104 0.7824637946866709 chr8 146364022 10926046 0.07464980704069474 0.6565408983565176 chr9 141213431 9019820 0.06387366935373166 0.46157132250425836 chr10 135534747 10860063 0.08012751888635614 0.6870776389793306 chr11 135006516 10279394 0.07613998423602013 0.5269465923119717 chr12 133851895 9506753 0.07102441844398243 0.3829507114439588 chr13 115169878 9574101 0.0831302521654143 0.4045230866249691 chr14 107349540 6964825 0.06487987745452845 0.41612378692015844 chr15 102531392 6484893 0.06324787826932068 0.35048279521123005 chr16 90354753 7493692 0.08293633429555167 0.44039240355237536 chr17 81195210 5581278 0.06873900566301878 0.3837939846151744 chr18 78077248 3755902 0.04810494857605637 0.8321964611417425 chr19 59128983 4588436 0.07760045526235416 0.8427053699963756 chr20 63025520 4719440 0.07488141311646457 0.40543853945401737 chr21 48129895 4089799 0.08497419327426332 0.48522572560001326 chr22 51304566 2609171 0.050856506611906625 0.3250578968196111 chrMT 16571 67969 4.101683664232696 3.709092162655939 chrX 155270560 12858697 0.08281477828121442 0.44308216946456325 chrY 59373566 740232 0.012467366369741039 0.37071358712206615