BamQC report ----------------------------------- >>>>>>> Input bam file = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam outfile = /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-153_S4_L002_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 = 13,399,110 number of mapped reads = 13,399,110 (100%) number of mapped paired reads (first in pair) = 6,699,555 number of mapped paired reads (second in pair) = 6,699,555 number of mapped paired reads (both in pair) = 13,399,110 number of mapped paired reads (singletons) = 0 number of mapped bases = 1,187,857,248 bp number of sequenced bases = 1,185,198,318 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,791,669 duplication rate = 31.8% >>>>>>> Insert size mean insert size = 142.0593 std insert size = 85.057 median insert size = 119 >>>>>>> Mapping quality mean mapping quality = 23.5555 >>>>>>> ACTG content number of A's = 455,135,605 bp (38.4%) number of C's = 138,909,338 bp (11.72%) number of T's = 453,669,198 bp (38.28%) number of G's = 137,484,177 bp (11.6%) number of N's = 64,695 bp (0.01%) GC percentage = 23.32% >>>>>>> Mismatches and indels general error rate = 0.1865 number of mismatches = 216,404,456 number of insertions = 1,478,476 mapped reads with insertion percentage = 9.61% number of deletions = 1,395,172 mapped reads with deletion percentage = 9.4% homopolymer indels = 48.09% >>>>>>> Coverage mean coverageData = 1.2605X std coverageData = 8.0758X There is a 33.74% of reference with a coverageData >= 1X There is a 22.25% of reference with a coverageData >= 2X There is a 13.89% of reference with a coverageData >= 3X There is a 10.08% of reference with a coverageData >= 4X There is a 7.11% of reference with a coverageData >= 5X There is a 5.42% of reference with a coverageData >= 6X There is a 4.07% of reference with a coverageData >= 7X There is a 3.21% of reference with a coverageData >= 8X There is a 2.52% of reference with a coverageData >= 9X There is a 2.05% of reference with a coverageData >= 10X There is a 1.67% of reference with a coverageData >= 11X There is a 1.39% of reference with a coverageData >= 12X There is a 1.17% of reference with a coverageData >= 13X There is a 1% of reference with a coverageData >= 14X There is a 0.86% of reference with a coverageData >= 15X There is a 0.75% of reference with a coverageData >= 16X There is a 0.66% of reference with a coverageData >= 17X There is a 0.59% of reference with a coverageData >= 18X There is a 0.53% of reference with a coverageData >= 19X There is a 0.48% of reference with a coverageData >= 20X There is a 0.43% of reference with a coverageData >= 21X There is a 0.4% of reference with a coverageData >= 22X There is a 0.36% of reference with a coverageData >= 23X There is a 0.34% of reference with a coverageData >= 24X There is a 0.31% of reference with a coverageData >= 25X There is a 0.29% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig PGA_scaffold1__77_contigs__length_89643857 89643857 119795284 1.3363468285395173 7.611478569668414 PGA_scaffold2__36_contigs__length_69596280 69596280 95313973 1.3695268339054905 6.420152098242339 PGA_scaffold3__111_contigs__length_57743597 57743597 75429174 1.306277715951779 4.847392240434477 PGA_scaffold4__129_contigs__length_65288255 65288255 81268988 1.2447719425186046 6.310246573035657 PGA_scaffold5__109_contigs__length_67248332 67248332 73980167 1.1001041185675802 4.886747765639738 PGA_scaffold6__104_contigs__length_61759565 61759565 74050689 1.1990157152175538 10.399031393571168 PGA_scaffold7__69_contigs__length_43120122 43120122 53112287 1.231728588337482 4.503574552451135 PGA_scaffold8__63_contigs__length_61151155 61151155 77122632 1.2611802998651456 4.883851707887042 PGA_scaffold9__45_contigs__length_38581958 38581958 54013526 1.3999685034129166 11.6104112433455 PGA_scaffold10__49_contigs__length_53961475 53961475 62720144 1.1623133726422414 4.09010834794093 PGA_scaffold11__79_contigs__length_51449921 51449921 56667892 1.1014184453266702 5.070033589330287 PGA_scaffold12__71_contigs__length_50438331 50438331 67209918 1.332516692513081 5.881702931288628 PGA_scaffold13__52_contigs__length_44396874 44396874 55638044 1.2531973309652387 5.997206857779396 PGA_scaffold14__91_contigs__length_45393038 45393038 72385798 1.5946453727111192 20.167790698259857 PGA_scaffold15__101_contigs__length_47938513 47938513 50004918 1.0431053211850772 4.703142079097018 PGA_scaffold16__33_contigs__length_31980953 31980953 42782769 1.3377577897694293 13.582838533856396 PGA_scaffold17__51_contigs__length_34923512 34923512 44674532 1.2792107506255386 5.942977009418158 PGA_scaffold18__69_contigs__length_27737463 27737463 31686513 1.1423724296630877 7.059799745637523