BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818852.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,118,235 number of mapped reads = 2,088,799 (98.61%) number of supplementary alignments = 33,844 (1.6%) number of secondary alignments = 0 number of mapped bases = 193,268,651 bp number of sequenced bases = 193,147,985 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 576,401 duplication rate = 23.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3634 >>>>>>> ACTG content number of A's = 56,246,448 bp (29.12%) number of C's = 41,491,834 bp (21.48%) number of T's = 54,875,016 bp (28.41%) number of G's = 40,531,958 bp (20.98%) number of N's = 2,729 bp (0%) GC percentage = 42.47% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,163,548 number of insertions = 24,564 mapped reads with insertion percentage = 1.14% number of deletions = 63,056 mapped reads with deletion percentage = 2.95% homopolymer indels = 41.95% >>>>>>> Coverage mean coverageData = 0.0624X std coverageData = 0.7153X There is a 3.95% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.08% 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 17367324 0.06967815739163194 1.1091382111758754 chr2 243199373 14511016 0.0596671604083453 1.019338897731477 chr3 198022430 11669643 0.058930915048360934 0.34740548647238156 chr4 191154276 9947770 0.052040530864190554 0.44856648497148255 chr5 180915260 8449979 0.04670683390665884 0.3281668554545298 chr6 171115067 9563775 0.055890899426173854 0.36951717370582643 chr7 159138663 16720567 0.10506916851500757 1.505494216949733 chr8 146364022 16981821 0.11602455827566695 0.6248345346830608 chr9 141213431 8315277 0.05888446262593818 0.6154911374262272 chr10 135534747 8854450 0.06532974160493324 0.8874746336889218 chr11 135006516 8344087 0.06180506872720128 0.44578323231618394 chr12 133851895 7495448 0.05599807159995755 0.3446575807776959 chr13 115169878 5872788 0.0509923957720959 0.32133634093670566 chr14 107349540 7100161 0.06614058150598502 0.39388255600193695 chr15 102531392 5245220 0.051157210466819765 0.3216804109465761 chr16 90354753 4649124 0.05145411664176648 0.7455558341537368 chr17 81195210 4727992 0.05822993745567011 0.4302610318274775 chr18 78077248 3784975 0.04847731057324151 0.693975024811716 chr19 59128983 3215531 0.05438163886566424 0.9060382728027448 chr20 63025520 7971712 0.12648387510329148 0.5587665409799396 chr21 48129895 1885293 0.03917093523682111 0.3621350820888061 chr22 51304566 1725427 0.03363106121977525 0.3099614149073586 chrMT 16571 369347 22.288757467865548 13.415368615599109 chrX 155270560 7806108 0.050274230993950175 0.39079722935161315 chrY 59373566 693816 0.011685604331058707 0.8295493344228421