BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080722.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 = 4,066,222 number of mapped reads = 3,846,451 (94.6%) number of supplementary alignments = 23,685 (0.58%) number of secondary alignments = 0 number of mapped bases = 272,228,894 bp number of sequenced bases = 272,123,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 186,995 duplication rate = 4.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6401 >>>>>>> ACTG content number of A's = 80,424,005 bp (29.55%) number of C's = 51,040,296 bp (18.76%) number of T's = 85,842,089 bp (31.55%) number of G's = 54,813,255 bp (20.14%) number of N's = 3,941 bp (0%) GC percentage = 38.9% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 2,194,946 number of insertions = 19,515 mapped reads with insertion percentage = 0.5% number of deletions = 58,752 mapped reads with deletion percentage = 1.51% homopolymer indels = 48.73% >>>>>>> Coverage mean coverageData = 0.0879X std coverageData = 0.6035X There is a 6.27% of reference with a coverageData >= 1X There is a 1.68% of reference with a coverageData >= 2X There is a 0.49% 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% 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 33210012 0.1332394353392604 0.9569468414859906 chr2 243199373 18439672 0.07582121521341258 0.5262991975509683 chr3 198022430 17135817 0.08653472740436526 0.38378351371951536 chr4 191154276 11842903 0.06195468523026919 0.3362678159139026 chr5 180915260 12882781 0.07120892400121472 0.34326957211758247 chr6 171115067 16235603 0.09488120061338608 0.5884519676872303 chr7 159138663 17496686 0.10994616688466209 1.2967910663052726 chr8 146364022 34021870 0.23244694655903894 1.014586639765624 chr9 141213431 8416315 0.059599961139673745 0.41761725929049864 chr10 135534747 12928486 0.09538871976497658 0.5783757639746184 chr11 135006516 11557232 0.08560499405821272 0.4457006784332091 chr12 133851895 8435518 0.0630212818428906 0.3251598418462267 chr13 115169878 6030957 0.05236574966242475 0.2946506956037702 chr14 107349540 5218153 0.048608992642166886 0.29732581208041703 chr15 102531392 4538728 0.044266715895167015 0.26942092075948987 chr16 90354753 6189388 0.06850096751412735 0.3632146206054761 chr17 81195210 4268128 0.05256625360042791 0.3290554555550569 chr18 78077248 8494075 0.10879065563376414 0.7129402129780632 chr19 59128983 4034551 0.06823305247783477 0.5775235596128903 chr20 63025520 6600151 0.10472188091427091 0.42545271115656924 chr21 48129895 4145411 0.08612964977380483 0.39499198364853233 chr22 51304566 2251589 0.0438867176071619 0.26483205618108674 chrMT 16571 23587 1.4233902600929333 1.5144593911376483 chrX 155270560 17285867 0.11132739522546965 0.47390806788354345 chrY 59373566 545414 0.00918614185983035 0.15989590494100492