BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats/genome_results.txt >>>>>>> Reference number of bases = 942,353,201 bp number of contigs = 18 >>>>>>> Globals number of windows = 417 number of reads = 18,711,866 number of mapped reads = 18,711,866 (100%) number of mapped paired reads (first in pair) = 9,355,933 number of mapped paired reads (second in pair) = 9,355,933 number of mapped paired reads (both in pair) = 18,711,866 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,729,464,455 bp number of sequenced bases = 1,725,736,658 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,109,418 duplication rate = 27.5% >>>>>>> Insert size mean insert size = 166.9241 std insert size = 92.8011 median insert size = 144 >>>>>>> Mapping quality mean mapping quality = 25.0553 >>>>>>> ACTG content number of A's = 670,578,136 bp (38.86%) number of C's = 193,635,630 bp (11.22%) number of T's = 669,182,642 bp (38.78%) number of G's = 192,340,250 bp (11.15%) number of N's = 23,831 bp (0%) GC percentage = 22.37% >>>>>>> Mismatches and indels general error rate = 0.1861 number of mismatches = 315,510,581 number of insertions = 1,947,541 mapped reads with insertion percentage = 9.09% number of deletions = 1,981,063 mapped reads with deletion percentage = 9.57% homopolymer indels = 51.78% >>>>>>> Coverage mean coverageData = 1.8353X std coverageData = 7.3341X There is a 44.42% of reference with a coverageData >= 1X There is a 30.9% of reference with a coverageData >= 2X There is a 21.58% of reference with a coverageData >= 3X There is a 16.07% of reference with a coverageData >= 4X There is a 11.96% of reference with a coverageData >= 5X There is a 9.2% of reference with a coverageData >= 6X There is a 7.06% of reference with a coverageData >= 7X There is a 5.55% of reference with a coverageData >= 8X There is a 4.36% of reference with a coverageData >= 9X There is a 3.51% of reference with a coverageData >= 10X There is a 2.82% of reference with a coverageData >= 11X There is a 2.32% of reference with a coverageData >= 12X There is a 1.92% of reference with a coverageData >= 13X There is a 1.62% of reference with a coverageData >= 14X There is a 1.36% of reference with a coverageData >= 15X There is a 1.17% of reference with a coverageData >= 16X There is a 1.01% of reference with a coverageData >= 17X There is a 0.89% of reference with a coverageData >= 18X There is a 0.78% of reference with a coverageData >= 19X There is a 0.7% of reference with a coverageData >= 20X There is a 0.62% of reference with a coverageData >= 21X There is a 0.56% of reference with a coverageData >= 22X There is a 0.51% of reference with a coverageData >= 23X There is a 0.46% of reference with a coverageData >= 24X There is a 0.42% of reference with a coverageData >= 25X There is a 0.39% of reference with a coverageData >= 26X There is a 0.36% of reference with a coverageData >= 27X There is a 0.34% of reference with a coverageData >= 28X There is a 0.31% of reference with a coverageData >= 29X There is a 0.29% of reference with a coverageData >= 30X There is a 0.28% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 175302743 1.9555466360623015 4.783437224410479 PGA_scaffold2__36_contigs__length_69596280 69596280 138121614 1.9846120223667127 5.6917144824721975 PGA_scaffold3__111_contigs__length_57743597 57743597 110090481 1.9065400619223634 5.338549827557466 PGA_scaffold4__129_contigs__length_65288255 65288255 119781117 1.8346503057862398 6.711071097397427 PGA_scaffold5__109_contigs__length_67248332 67248332 107437618 1.5976250236214038 5.025243440328562 PGA_scaffold6__104_contigs__length_61759565 61759565 107223369 1.7361419077352633 7.6562460481160795 PGA_scaffold7__69_contigs__length_43120122 43120122 78180758 1.8130922264088214 4.916776018224595 PGA_scaffold8__63_contigs__length_61151155 61151155 112652959 1.842204926464594 5.590073256867569 PGA_scaffold9__45_contigs__length_38581958 38581958 77054600 1.9971666549427067 11.523507359407109 PGA_scaffold10__49_contigs__length_53961475 53961475 93010758 1.7236511418562965 4.4662598288646045 PGA_scaffold11__79_contigs__length_51449921 51449921 85407664 1.6600154546398622 5.557462038949302 PGA_scaffold12__71_contigs__length_50438331 50438331 97998289 1.9429328262269423 6.75195596102827 PGA_scaffold13__52_contigs__length_44396874 44396874 80368231 1.8102227422588355 5.617626216926822 PGA_scaffold14__91_contigs__length_45393038 45393038 103045112 2.270064233198051 18.508446578363316 PGA_scaffold15__101_contigs__length_47938513 47938513 73320712 1.5294740577372519 4.983701795944819 PGA_scaffold16__33_contigs__length_31980953 31980953 60637341 1.896045468063444 10.10609304998366 PGA_scaffold17__51_contigs__length_34923512 34923512 64802358 1.8555510110208848 5.141668339343748 PGA_scaffold18__69_contigs__length_27737463 27737463 45028731 1.6233903944279258 6.238419012139139